# Date 2008-01-16 Time 05:46:12 PST -0800 (1200491172.25 s)
#phil __OFF__

Command line arguments: "../869.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31103
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 869

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95111
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.9411

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95111
Completeness in resolution range: 0.943912
Completeness with d_max=infinity: 0.9411

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1761 [2170/2199]  1957   213   9.8%
  bin  2:  4.1761 -  3.3266 [2101/2117]  1888   213  10.1%
  bin  3:  3.3266 -  2.9096 [2051/2070]  1842   209  10.2%
  bin  4:  2.9096 -  2.6451 [2054/2084]  1858   196   9.5%
  bin  5:  2.6451 -  2.4564 [2044/2063]  1837   207  10.1%
  bin  6:  2.4564 -  2.3122 [2032/2057]  1821   211  10.4%
  bin  7:  2.3122 -  2.1967 [2006/2040]  1808   198   9.9%
  bin  8:  2.1967 -  2.1014 [2004/2034]  1804   200  10.0%
  bin  9:  2.1014 -  2.0207 [2004/2046]  1808   196   9.8%
  bin 10:  2.0207 -  1.9511 [1123/2043]  1007   116  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/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:
        1.65 -     2.30: 29
        2.30 -     2.95: 1701
        2.95 -     3.60: 4611
        3.60 -     4.25: 9339
        4.25 -     4.90: 13053
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.649 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.667 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.708 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.782 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28728 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_869/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 84.23025 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4580   r_free= 0.4619   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.265101                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.3654 0.3672      6.5307      6.5474|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.3916 0.3672      6.7812      6.7444|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.4339 0.4396      6.6525      6.7464|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.4367 0.4446      6.5063      6.4728|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.4806 0.4497      6.3501      6.3325|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.4952 0.5288      6.2668       6.273|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.4919 0.4863      6.2367      6.1884|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.4985 0.4847      6.1537      6.1691|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.4968 0.4694      6.1175      6.0845|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.5026 0.5487      6.0735      6.1109|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.5114 0.6106      6.0395       6.061|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.5174 0.5424      5.9487      5.9917|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.5211 0.4859      5.8848      5.8105|
| 14:  1.9998 -  1.9511 0.43    565   58 0.5479 0.5069      5.8307      5.8406|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6584  1410   159  0.72  32.82   0.83     0.76      65161.20|
|  2:  4.6584 -  3.7160  1364   145  0.72  33.92   0.92     0.84     100056.63|
|  3:  3.7160 -  3.2518  1327   151  0.61  42.68   0.93     0.81     109748.29|
|  4:  3.2518 -  2.9569  1338   151  0.52  50.52   0.95     0.73     101966.84|
|  5:  2.9569 -  2.7464  1316   146  0.43  57.10   0.89     0.62      80572.83|
|  6:  2.7464 -  2.5853  1312   149  0.40  59.71   0.90     0.57      71010.93|
|  7:  2.5853 -  2.4564  1315   137  0.40  59.87   0.94     0.54      61964.21|
|  8:  2.4564 -  2.3499  1293   150  0.40  59.66   0.91     0.59      55691.40|
|  9:  2.3499 -  2.2598  1298   146  0.40  60.14   0.95     0.58      50945.50|
| 10:  2.2598 -  2.1820  1291   141  0.35  63.60   0.95     0.53      50043.04|
| 11:  2.1820 -  2.1140  1299   139  0.28  68.94   0.96     0.44      50368.37|
| 12:  2.1140 -  2.0537  1266   146  0.27  70.30   0.96     0.43      45669.89|
| 13:  2.0537 -  1.9998  1236   141  0.28  69.18   0.95     0.45      38840.34|
| 14:  1.9998 -  1.9511   565    58  0.31  66.79   0.92     0.47      31493.38|
|alpha:            min =        0.43 max =            0.84 mean =         0.61|
|beta:             min =    31493.38 max =       109748.29 mean =     67095.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.05|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.31|
|-----------------------------------------------------------------------------|

============================== 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 = 10.382889             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.611265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.924   (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 |  1.649 -  1.974:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.974 -  2.299:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.299 -  2.624:       77 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.624 -  2.949:     1624 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.949 -  3.274:     1964 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.274 -  3.600:     2647 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.600 -  3.925:     4815 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.925 -  4.250:     4524 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.250 -  4.575:     5961 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.575 -  4.900:     7092 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| 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  1.649 |       0.467 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4580   r_free= 0.4619   ksol= 0.00   Bsol= 0.00   scale= 0.910    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.265101                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4485   r_free= 0.4537   ksol= 0.30   Bsol= 20.00   scale= 0.941   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,0.56,2.17,0.00,0.00,0.00); trace/3= 0.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.261911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.672647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.052   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.165552              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.697   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4485      final r-factor (work) = 0.3376          |
| start r-factor (free) = 0.4537      final r-factor (free) = 0.3652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1793 = 7.67 * 0.50 * 6.2558 + 1.00 * 0.1800                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6393 = 7.67 * 0.50 * 6.1315 + 1.00 * 0.1168                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3376      final r-factor (work) = 0.3073          |
| start r-factor (free) = 0.3652      final r-factor (free) = 0.3745          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1526 = 1.17 * 1.00 * 6.1315 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0153 = 1.17 * 1.00 * 6.0030 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.50   18.75    None  None   None       |
|    all(noH): 2823   0      0.00    89.50   18.75    None  None   None       |
|    Sol.    : 438    0      0.00    88.90   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    89.50   14.98    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:     0.000 -   8.950:  802   |   5:    44.751 -  53.701:   90        |
|      1:     8.950 -  17.900:  893   |   6:    53.701 -  62.651:   58        |
|      2:    17.900 -  26.851:  507   |   7:    62.651 -  71.602:   33        |
|      3:    26.851 -  35.801:  267   |   8:    71.602 -  80.552:   17        |
|      4:    35.801 -  44.751:  150   |   9:    80.552 -  89.502:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3073 r_free = 0.3745             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3069 r_free = 0.3752             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3069   r_free= 0.3752   ksol= 0.30   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,0.56,2.17,0.00,0.00,0.00); trace/3= 0.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.007570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3062   r_free= 0.3743   ksol= 0.33   Bsol= 44.56   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.83,0.60,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.008363                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.982659              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335378              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.391  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3062      final r-factor (work) = 0.2298          |
| start r-factor (free) = 0.3743      final r-factor (free) = 0.2930          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0754 = 5.98 * 0.50 * 6.0036 + 1.00 * 0.1168                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7414 = 5.98 * 0.50 * 5.9034 + 1.00 * 0.0823                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2298      final r-factor (work) = 0.2104          |
| start r-factor (free) = 0.2930      final r-factor (free) = 0.2724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9980 = 0.34 * 1.00 * 5.9034 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9351 = 0.34 * 1.00 * 5.7368 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.87   17.66    None  None   None       |
|    all(noH): 2823   0      0.00    84.87   17.66    None  None   None       |
|    Sol.    : 438    0      3.27    84.87   39.52    None  None   None       |
|    Mac.    : 2385   0      0.00    83.99   13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.487:  697   |   5:    42.437 -  50.925:  119        |
|      1:     8.487 -  16.975: 1178   |   6:    50.925 -  59.412:   63        |
|      2:    16.975 -  25.462:  380   |   7:    59.412 -  67.899:   35        |
|      3:    25.462 -  33.950:  186   |   8:    67.899 -  76.387:   13        |
|      4:    33.950 -  42.437:  147   |   9:    76.387 -  84.874:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2104 r_free = 0.2724             target_work(ml) = 5.701         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2101 r_free = 0.2720             target_work(ml) = 5.700         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2101   r_free= 0.2720   ksol= 0.33   Bsol= 44.56   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.83,0.60,-0.00,0.00,0.00); trace/3= -0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.700107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2098   r_free= 0.2711   ksol= 0.33   Bsol= 42.50   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.92,-0.71,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.697851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.544300              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.376   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211726              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.098   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2098      final r-factor (work) = 0.1597          |
| start r-factor (free) = 0.2711      final r-factor (free) = 0.2080          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2501 = 3.54 * 0.50 * 5.7376 + 1.00 * 0.0823                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9548 = 3.54 * 0.50 * 5.5852 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1597      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2080      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1965 = 0.21 * 1.00 * 5.5852 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1711 = 0.21 * 1.00 * 5.4179 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.59   17.65    None  None   None       |
|    all(noH): 2823   0      0.00    84.59   17.65    None  None   None       |
|    Sol.    : 438    0      5.08    84.59   39.72    None  None   None       |
|    Mac.    : 2385   0      0.00    83.81   13.60    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 -   8.459:  639   |   5:    42.294 -  50.752:  124        |
|      1:     8.459 -  16.918: 1276   |   6:    50.752 -  59.211:   62        |
|      2:    16.918 -  25.376:  347   |   7:    59.211 -  67.670:   34        |
|      3:    25.376 -  33.835:  176   |   8:    67.670 -  76.129:   15        |
|      4:    33.835 -  42.294:  145   |   9:    76.129 -  84.587:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1518 r_free = 0.2006             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1516 r_free = 0.2002             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1516   r_free= 0.2002   ksol= 0.33   Bsol= 42.50   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.92,-0.71,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.398918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1515   r_free= 0.2002   ksol= 0.32   Bsol= 42.50   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.65,-1.68,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.398270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.591920              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.699  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.790130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.785   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1515      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.2002      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0821 = 2.59 * 0.50 * 5.4208 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9776 = 2.59 * 0.50 * 5.3405 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2321 = 0.79 * 1.00 * 5.3405 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1476 = 0.79 * 1.00 * 5.2375 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    94.82   17.78    None  None   None       |
|    all(noH): 2823   0      1.24    94.82   17.78    None  None   None       |
|    Sol.    : 438    0      5.28    83.92   42.65    None  None   None       |
|    Mac.    : 2385   0      1.24    94.82   13.22    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:     1.238 -  10.595: 1124   |   5:    48.026 -  57.384:  113        |
|      1:    10.595 -  19.953: 1030   |   6:    57.384 -  66.742:   55        |
|      2:    19.953 -  29.311:  227   |   7:    66.742 -  76.100:   34        |
|      3:    29.311 -  38.669:  122   |   8:    76.100 -  85.458:   10        |
|      4:    38.669 -  48.026:  106   |   9:    85.458 -  94.815:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1671             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1670             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1670   ksol= 0.32   Bsol= 42.50   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.65,-1.68,-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: 5.205431                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1670   ksol= 0.32   Bsol= 43.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.74,-1.95,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.881357              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.849  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.448793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.565  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9831 = 1.88 * 0.50 * 5.2372 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9297 = 1.88 * 0.50 * 5.1846 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3361 = 0.45 * 1.00 * 5.1846 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3268 = 0.45 * 1.00 * 5.1646 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    99.82   17.52    None  None   None       |
|    all(noH): 2823   0      1.36    99.82   17.52    None  None   None       |
|    Sol.    : 438    0      6.26    90.50   41.75    None  None   None       |
|    Mac.    : 2385   0      1.36    99.82   13.06    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:     1.357 -  11.203: 1279   |   5:    50.587 -  60.433:   86        |
|      1:    11.203 -  21.049:  941   |   6:    60.433 -  70.279:   41        |
|      2:    21.049 -  30.895:  200   |   7:    70.279 -  80.125:   25        |
|      3:    30.895 -  40.741:  124   |   8:    80.125 -  89.971:    6        |
|      4:    40.741 -  50.587:  118   |   9:    89.971 -  99.817:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1603             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1601             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1601   ksol= 0.32   Bsol= 43.18   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.74,-1.95,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155865                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.0989 0.1284      5.3753      5.5483|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.0872 0.1175      5.4536      5.6835|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.1116 0.1596      5.5109      5.8623|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.1288 0.1647      5.4948      5.6275|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.1320 0.1673      5.3033      5.4737|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.1207 0.1657      5.1844      5.4022|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.1264 0.1717      5.1617      5.3676|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.1174 0.1787      5.0434      5.3756|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.1169 0.1829      5.0286      5.3147|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.1146 0.1785      4.9472      5.2222|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.1184 0.1860      4.9646      5.3116|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.1119 0.1634      4.8805      5.0802|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.1212 0.1837      4.8172      5.0601|
| 14:  1.9998 -  1.9511 0.43    565   58 0.1065 0.1507      4.6537      4.9372|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6584  1410   159  0.94   8.56   0.98     0.96       6575.81|
|  2:  4.6584 -  3.7160  1364   145  0.95   8.10   1.02     1.01       9154.12|
|  3:  3.7160 -  3.2518  1327   151  0.93  11.98   1.04     1.04      11060.78|
|  4:  3.2518 -  2.9569  1338   151  0.91  14.38   1.02     0.99      10845.27|
|  5:  2.9569 -  2.7464  1316   146  0.90  15.50   1.00     0.97       7689.68|
|  6:  2.7464 -  2.5853  1312   149  0.90  15.48   0.99     0.98       6598.42|
|  7:  2.5853 -  2.4564  1315   137  0.91  15.13   1.00     0.98       6022.53|
|  8:  2.4564 -  2.3499  1293   150  0.91  14.96   0.98     0.95       4934.80|
|  9:  2.3499 -  2.2598  1298   146  0.91  15.33   1.01     0.99       4962.38|
| 10:  2.2598 -  2.1820  1291   141  0.91  15.31   1.00     0.97       4228.31|
| 11:  2.1820 -  2.1140  1299   139  0.89  17.15   1.00     0.96       4595.03|
| 12:  2.1140 -  2.0537  1266   146  0.91  15.86   1.01     1.00       4082.54|
| 13:  2.0537 -  1.9998  1236   141  0.90  16.12   1.01     1.00       3405.26|
| 14:  1.9998 -  1.9511   565    58  0.91  14.87   0.99     0.96       2485.17|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2485.17 max =        11060.78 mean =      6391.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.10|
|phase err.(test): min =        0.00 max =           89.05 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1597   ksol= 0.32   Bsol= 43.48   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.65,-1.94,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1597   ksol= 0.32   Bsol= 43.48   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.65,-1.94,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156349                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6584 0.99   1410  159 0.0982 0.1264      5.3693      5.5363|
|  2:  4.6584 -  3.7160 0.99   1364  145 0.0890 0.1170      5.4618      5.6887|
|  3:  3.7160 -  3.2518 0.99   1327  151 0.1121 0.1607      5.5125      5.8674|
|  4:  3.2518 -  2.9569 0.99   1338  151 0.1291 0.1643      5.4977      5.6292|
|  5:  2.9569 -  2.7464 0.99   1316  146 0.1327 0.1663      5.3058      5.4708|
|  6:  2.7464 -  2.5853 0.99   1312  149 0.1212 0.1662      5.1857       5.408|
|  7:  2.5853 -  2.4564 0.99   1315  137 0.1265 0.1711      5.1623      5.3671|
|  8:  2.4564 -  2.3499 0.98   1293  150 0.1168 0.1792      5.0436      5.3785|
|  9:  2.3499 -  2.2598 0.98   1298  146 0.1167 0.1823      5.0278      5.3126|
| 10:  2.2598 -  2.1820 0.99   1291  141 0.1145 0.1777      4.9452      5.2175|
| 11:  2.1820 -  2.1140 0.99   1299  139 0.1182 0.1862      4.9633      5.3107|
| 12:  2.1140 -  2.0537 0.97   1266  146 0.1118 0.1636      4.8803       5.082|
| 13:  2.0537 -  1.9998 0.95   1236  141 0.1211 0.1835      4.8171       5.059|
| 14:  1.9998 -  1.9511 0.43    565   58 0.1064 0.1512       4.653        4.94|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6584  1410   159  0.94   8.72   0.98     0.96       6611.18|
|  2:  4.6584 -  3.7160  1364   145  0.95   8.11   1.03     1.02       9106.25|
|  3:  3.7160 -  3.2518  1327   151  0.93  11.97   1.04     1.04      11016.98|
|  4:  3.2518 -  2.9569  1338   151  0.91  14.47   1.02     0.99      10957.13|
|  5:  2.9569 -  2.7464  1316   146  0.90  15.55   1.00     0.97       7699.69|
|  6:  2.7464 -  2.5853  1312   149  0.90  15.54   0.99     0.98       6613.55|
|  7:  2.5853 -  2.4564  1315   137  0.91  15.17   1.00     0.98       6042.52|
|  8:  2.4564 -  2.3499  1293   150  0.91  14.99   0.99     0.95       4957.61|
|  9:  2.3499 -  2.2598  1298   146  0.91  15.32   1.01     0.99       4950.01|
| 10:  2.2598 -  2.1820  1291   141  0.91  15.29   1.00     0.97       4219.01|
| 11:  2.1820 -  2.1140  1299   139  0.89  17.12   1.00     0.96       4580.97|
| 12:  2.1140 -  2.0537  1266   146  0.91  15.87   1.02     1.01       4087.39|
| 13:  2.0537 -  1.9998  1236   141  0.90  16.14   1.01     1.00       3410.32|
| 14:  1.9998 -  1.9511   565    58  0.91  14.87   0.99     0.96       2484.80|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2484.80 max =        11016.98 mean =      6398.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.99 mean =        13.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    99.77   17.47    None  None   None       |
|    all(noH): 2823   0      1.31    99.77   17.47    None  None   None       |
|    Sol.    : 438    0      6.22    90.45   41.70    None  None   None       |
|    Mac.    : 2385   0      1.31    99.77   13.02    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:     1.309 -  11.155: 1279   |   5:    50.539 -  60.385:   86        |
|      1:    11.155 -  21.001:  941   |   6:    60.385 -  70.231:   41        |
|      2:    21.001 -  30.847:  200   |   7:    70.231 -  80.077:   25        |
|      3:    30.847 -  40.693:  124   |   8:    80.077 -  89.923:    6        |
|      4:    40.693 -  50.539:  118   |   9:    89.923 -  99.770:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.655 - 5.731
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 314
   mapped sites are within: 0.721 - 5.731

peak=    6.286 closest distance to " O   HOH Z 278 " =    1.332
peak=    6.124 closest distance to " NE2 GLN A  11 " =    1.280
peak=    5.563 closest distance to " O   HOH Z 214 " =    1.444
peak=    5.549 closest distance to " NH2 ARG A  56 " =    2.070
peak=    5.432 closest distance to " CG  PRO A 213 " =    1.283
peak=    5.410 closest distance to " CG  PRO A  54 " =    1.259
peak=    5.313 closest distance to " O   HOH Z   7 " =    1.428
peak=    5.216 closest distance to " O   HOH Z 134 " =    1.616
peak=    5.205 closest distance to " O   HOH Z 260 " =    1.400
peak=    5.125 closest distance to " CG  PRO A 198 " =    1.340
peak=    5.057 closest distance to " O   HOH Z 144 " =    1.767
peak=    5.055 closest distance to " CB  GLN A 223 " =    1.516
peak=    5.012 closest distance to " O   HOH Z 126 " =    1.918
peak=    4.892 closest distance to " O   HOH Z 236 " =    1.405
peak=    4.761 closest distance to " CB  SER A  63 " =    1.267
peak=    4.717 closest distance to " CB  ASN A 148 " =    1.421
peak=    4.692 closest distance to " O   HOH Z 427 " =    2.508
peak=    4.641 closest distance to " O   HOH Z 298 " =    1.903
peak=    4.606 closest distance to " CB  ARG A 275 " =    0.904
peak=    4.602 closest distance to " O   HOH Z 193 " =    1.835
peak=    4.568 closest distance to " CB  SER A   3 " =    1.452
peak=    4.480 closest distance to " O   HOH Z 132 " =    1.182
peak=    4.467 closest distance to " CG  PRO A  90 " =    1.163
peak=    4.464 closest distance to " O   HOH Z 423 " =    1.735
peak=    4.456 closest distance to " O   HOH Z 221 " =    1.775
peak=    4.428 closest distance to " O   HOH Z  78 " =    1.772
peak=    4.408 closest distance to " O   HOH Z 207 " =    1.707
peak=    4.392 closest distance to " O   HOH Z 232 " =    2.221
peak=    4.383 closest distance to " CA  GLY A 241 " =    3.628
peak=    4.356 closest distance to " CB  TYR A 169 " =    0.803
peak=    4.335 closest distance to " CB  GLN A 183 " =    1.190
peak=    4.317 closest distance to " O   HOH Z  11 " =    1.802
peak=    4.313 closest distance to " CB  TRP A 179 " =    1.370
peak=    4.310 closest distance to " O   HOH Z 124 " =    1.399
peak=    4.297 closest distance to " O   HOH Z 369 " =    2.103
peak=    4.260 closest distance to " O   HOH Z 202 " =    1.302
peak=    4.258 closest distance to " O   HOH Z 425 " =    1.394
peak=    4.258 closest distance to " O   HOH Z 352 " =    1.860
peak=    4.250 closest distance to " O   PRO A 198 " =    1.556
peak=    4.248 closest distance to " O   HOH Z 403 " =    1.429
peak=    4.240 closest distance to " O   HOH Z 287 " =    1.855
peak=    4.239 closest distance to " CB  GLU A 152 " =    1.320
peak=    4.238 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.207 closest distance to " O   HOH Z  10 " =    1.842
peak=    4.195 closest distance to " ND2 ASN A 187 " =    1.597
peak=    4.190 closest distance to " O   HOH Z 316 " =    3.054
peak=    4.189 closest distance to " CB  PRO A  54 " =    0.919
peak=    4.182 closest distance to " CG2 VAL A 257 " =    0.892
peak=    4.179 closest distance to " O   HOH Z 217 " =    2.963
peak=    4.155 closest distance to " O   HOH Z 193 " =    1.660
peak=    4.154 closest distance to " O   HOH Z  97 " =    1.181
peak=    4.138 closest distance to " O   HOH Z 272 " =    1.835
peak=    4.124 closest distance to " O   HOH Z 126 " =    1.546
peak=    4.120 closest distance to " O   HOH Z 183 " =    1.383
peak=    4.114 closest distance to " CB  ARG A 139 " =    1.086
peak=    4.113 closest distance to " O   HOH Z  44 " =    1.794
peak=    4.112 closest distance to " O   HOH Z 108 " =    1.748
peak=    4.104 closest distance to " OD1 ASN A  69 " =    2.675
peak=    4.084 closest distance to " O   HOH Z  97 " =    1.979
peak=    4.061 closest distance to " CA  TYR A  30 " =    0.984
peak=    4.053 closest distance to " OD2 ASP A 286 " =    2.670
peak=    4.053 closest distance to " O   HOH Z 371 " =    1.825
peak=    4.020 closest distance to " O   SER A  87 " =    2.349
peak=    4.019 closest distance to " O   HOH Z   3 " =    2.083
peak=    4.013 closest distance to " O   HOH Z 263 " =    2.283
peak=    4.010 closest distance to " CG1 ILE A  33 " =    1.217
peak=    4.008 closest distance to " CB  LEU A 228 " =    1.136
peak=    3.978 closest distance to " O   HOH Z 419 " =    2.148
peak=    3.940 closest distance to " O   HOH Z 368 " =    1.903
peak=    3.938 closest distance to " NH2BARG A 102 " =    1.007
peak=    3.930 closest distance to " O   HOH Z 261 " =    1.697
peak=    3.930 closest distance to " O   HOH Z 247 " =    1.277
peak=    3.924 closest distance to " CA  THR A 264 " =    0.787
peak=    3.876 closest distance to " O   HOH Z 135 " =    1.699
peak=    3.847 closest distance to " O   HOH Z 234 " =    3.691
peak=    3.839 closest distance to " O   HOH Z  15 " =    2.257
peak=    3.836 closest distance to " O   HOH Z  61 " =    1.648
peak=    3.822 closest distance to " N   PHE A 130 " =    1.288
peak=    3.817 closest distance to " O   HOH Z  49 " =    1.341
peak=    3.811 closest distance to " O   HOH Z  21 " =    1.694
peak=    3.808 closest distance to " CD  LYS A 119 " =    1.140
peak=    3.806 closest distance to " O   HOH Z  68 " =    1.618
peak=    3.803 closest distance to " CG  TRP A 179 " =    2.235
peak=    3.801 closest distance to " O   HOH Z 409 " =    2.193
peak=    3.784 closest distance to " O   HOH Z  88 " =    3.153
peak=    3.776 closest distance to " CD BLYS A 290 " =    1.110
peak=    3.772 closest distance to " O   HOH Z  59 " =    1.591
peak=    3.771 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.771 closest distance to " CG2 THR A 221 " =    1.135
peak=    3.764 closest distance to " CA  ALA A 154 " =    0.985
peak=    3.758 closest distance to " O   HOH Z  48 " =    1.531
peak=    3.749 closest distance to " CG  ARG A  66 " =    2.309
peak=    3.749 closest distance to " O   HOH Z 132 " =    1.998
peak=    3.747 closest distance to " O   HOH Z 344 " =    3.026
peak=    3.746 closest distance to " CA  ALA A  21 " =    1.136
peak=    3.744 closest distance to " O   HOH Z 227 " =    1.776
peak=    3.740 closest distance to " CB  ARG A 102 " =    0.820
peak=    3.739 closest distance to " O   HOH Z 365 " =    2.723
peak=    3.729 closest distance to " O   HOH Z 394 " =    1.512
peak=    3.729 closest distance to " O   HOH Z   1 " =    1.817
peak=    3.726 closest distance to " CA  GLU A 152 " =    1.262
peak=    3.709 closest distance to " N   ARG A 156 " =    1.283
peak=    3.680 closest distance to " O   HOH Z  63 " =    1.418
peak=    3.676 closest distance to " O   HOH Z 368 " =    3.645
peak=    3.675 closest distance to " O   HOH Z  43 " =    1.863
peak=    3.663 closest distance to " NE AARG A 275 " =    1.445
peak=    3.661 closest distance to " O   HOH Z 133 " =    1.431
peak=    3.660 closest distance to " NH1AARG A 145 " =    1.009
peak=    3.658 closest distance to " O   HOH Z 271 " =    2.183
peak=    3.646 closest distance to " O   HOH Z 380 " =    1.535
peak=    3.645 closest distance to " O   HOH Z 334 " =    1.472
peak=    3.644 closest distance to " O   HOH Z 155 " =    1.652
peak=    3.639 closest distance to " OD1BASN A 224 " =    2.148
peak=    3.638 closest distance to " CB  VAL A 202 " =    1.639
peak=    3.633 closest distance to " O   HOH Z 195 " =    1.420
peak=    3.631 closest distance to " O   HOH Z 108 " =    1.966
peak=    3.628 closest distance to " O   HOH Z 391 " =    2.968
peak=    3.622 closest distance to " CG  PRO A 280 " =    0.823
peak=    3.615 closest distance to " CB  ALA A 291 " =    1.405
peak=    3.604 closest distance to " O   MET A 105 " =    1.745
peak=    3.602 closest distance to " NH2AARG A 190 " =    1.347
peak=    3.594 closest distance to " CB  THR A 157 " =    1.034
peak=    3.593 closest distance to " CD  LYS A 166 " =    1.350
peak=    3.584 closest distance to " O   HOH Z 313 " =    1.723
peak=    3.583 closest distance to " CG  PRO A 243 " =    1.085
peak=    3.578 closest distance to " OG  SER A  62 " =    3.159
peak=    3.576 closest distance to " O   SER A  26 " =    1.558
peak=    3.574 closest distance to " O   HOH Z  59 " =    2.004
peak=    3.570 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.566 closest distance to " CB  ALA A  34 " =    1.120
peak=    3.557 closest distance to " CG  GLN A  77 " =    2.231
peak=    3.551 closest distance to " CG  LEU A 167 " =    1.184
peak=    3.548 closest distance to " CB  TRP A 266 " =    1.032
peak=    3.543 closest distance to " CA  LEU A 282 " =    1.220
peak=    3.541 closest distance to " O   HOH Z 392 " =    1.328
peak=    3.535 closest distance to " O   HOH Z  73 " =    1.699
peak=    3.526 closest distance to " O   HOH Z 276 " =    1.301
peak=    3.506 closest distance to " N   GLN A 278 " =    0.928
peak=    3.502 closest distance to " O   HOH Z   6 " =    2.057
peak=    3.502 closest distance to " O   HOH Z   1 " =    1.653
peak=    3.502 closest distance to " O   HOH Z  93 " =    2.127
peak=    3.500 closest distance to " O   HOH Z 128 " =    1.944
peak=    3.489 closest distance to " O   HOH Z 180 " =    2.029
peak=    3.479 closest distance to " CA  ALA A 299 " =    0.964
peak=    3.478 closest distance to " O   HOH Z 405 " =    1.232
peak=    3.475 closest distance to " CB  ILE A 234 " =    0.977
peak=    3.475 closest distance to " O   HOH Z 374 " =    2.644
peak=    3.474 closest distance to " NH2 ARG A 219 " =    1.836
peak=    3.471 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.470 closest distance to " O   HOH Z 188 " =    2.017
peak=    3.469 closest distance to " CD  ARG A 138 " =    0.763
peak=    3.462 closest distance to " O   HOH Z 291 " =    1.983
peak=    3.462 closest distance to " CA  MET A  40 " =    1.090
peak=    3.461 closest distance to " O   HOH Z 151 " =    1.620
peak=    3.454 closest distance to " CB  SER A 216 " =    0.824
peak=    3.453 closest distance to " CA  LYS A  48 " =    1.417
peak=    3.447 closest distance to " O   HOH Z 284 " =    1.517
peak=    3.446 closest distance to " O   HOH Z 344 " =    1.102
peak=    3.437 closest distance to " O   HOH Z 189 " =    1.681
peak=    3.434 closest distance to " O   HOH Z 209 " =    2.156
peak=    3.432 closest distance to " CA  ASN A 215 " =    1.242
peak=    3.426 closest distance to " CB  ARG A  79 " =    1.389
peak=    3.422 closest distance to " CD2 LEU A 255 " =    1.458
peak=    3.419 closest distance to " CA  THR A 221 " =    0.897
peak=    3.418 closest distance to " ND1 HIS A  86 " =    1.882
peak=    3.417 closest distance to " O   HOH Z 193 " =    2.078
peak=    3.416 closest distance to " O   HOH Z 346 " =    1.544
peak=    3.413 closest distance to " O   HOH Z 133 " =    2.310
peak=    3.411 closest distance to " CB  ALA A   1 " =    4.544
peak=    3.407 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.406 closest distance to " CB  GLU A 277 " =    3.526
peak=    3.405 closest distance to " CA  VAL A  41 " =    0.953
peak=    3.403 closest distance to " CD  ARG A 159 " =    0.761
peak=    3.401 closest distance to " CB  TYR A 116 " =    0.930
peak=    3.396 closest distance to " CB  PRO A 198 " =    0.935
peak=    3.396 closest distance to " N   TYR A  15 " =    0.979
peak=    3.379 closest distance to " C   GLU A 277 " =    1.333
peak=    3.378 closest distance to " O   HOH Z 423 " =    2.151
peak=    3.375 closest distance to " CE1 TYR A 186 " =    1.322
peak=    3.374 closest distance to " OG  SER A  62 " =    2.967
peak=    3.366 closest distance to " O   HOH Z 153 " =    1.719
peak=    3.364 closest distance to " O   HOH Z 128 " =    1.485
peak=    3.363 closest distance to " O   HOH Z 437 " =    1.993
peak=    3.358 closest distance to " N   ASN A  39 " =    1.304
peak=    3.354 closest distance to " O   HOH Z  40 " =    2.198
peak=    3.354 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.354 closest distance to " O   HOH Z 258 " =    2.220
peak=    3.352 closest distance to " CA  GLY A 267 " =    1.321
peak=    3.348 closest distance to " CB  THR A  31 " =    1.635
peak=    3.348 closest distance to " O   HOH Z 295 " =    1.497
peak=    3.345 closest distance to " CA  ALA A 160 " =    0.828
peak=    3.343 closest distance to " CD1 LEU A 300 " =    1.184
peak=    3.342 closest distance to " O   HOH Z 116 " =    2.897
peak=    3.339 closest distance to " NH1 ARG A  14 " =    1.013
peak=    3.331 closest distance to " O   HOH Z 106 " =    2.322
peak=    3.330 closest distance to " O   HOH Z 353 " =    2.508
peak=    3.330 closest distance to " CG  GLN A  88 " =    1.052
peak=    3.329 closest distance to " O   HOH Z 227 " =    2.001
peak=    3.329 closest distance to " O   HOH Z 213 " =    2.048
peak=    3.327 closest distance to " O   HOH Z 172 " =    3.244
peak=    3.323 closest distance to " O   GLN A 278 " =    1.473
peak=    3.322 closest distance to " O   HOH Z 281 " =    1.849
peak=    3.322 closest distance to " CB  ARG A 190 " =    1.766
peak=    3.320 closest distance to " NZ  LYS A  76 " =    1.339
peak=    3.319 closest distance to " O   HOH Z 244 " =    1.691
peak=    3.319 closest distance to " O   HOH Z  44 " =    3.284
peak=    3.317 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.317 closest distance to " CB  LEU A 255 " =    0.835
peak=    3.315 closest distance to " CB  SER A 276 " =    1.112
peak=    3.315 closest distance to " O   HOH Z 373 " =    1.498
peak=    3.309 closest distance to " O   HOH Z 379 " =    1.951
peak=    3.308 closest distance to " CA  SER A  32 " =    1.624
peak=    3.305 closest distance to " CE AMET A  47 " =    1.400
peak=    3.300 closest distance to " N   ALA A   1 " =    2.113
peak=    3.299 closest distance to " O   HOH Z 194 " =    2.028
peak=    3.299 closest distance to " O   HOH Z 152 " =    2.488
peak=    3.298 closest distance to " O   HOH Z  64 " =    1.890
peak=    3.298 closest distance to " O   HOH Z 334 " =    2.810
peak=    3.297 closest distance to " O   HOH Z 286 " =    2.399
peak=    3.294 closest distance to " O   HOH Z 140 " =    1.398
peak=    3.294 closest distance to " CG  GLU A 277 " =    2.250
peak=    3.294 closest distance to " O   HOH Z 173 " =    1.953
peak=    3.294 closest distance to " O   HOH Z 410 " =    1.827
peak=    3.291 closest distance to " CB  MET A 105 " =    1.327
peak=    3.287 closest distance to " CA  LYS A 290 " =    1.324
peak=    3.286 closest distance to " O   HOH Z 122 " =    1.403
peak=    3.283 closest distance to " O   HOH Z 217 " =    1.417
peak=    3.282 closest distance to " CA  TYR A 186 " =    1.509
peak=    3.282 closest distance to " NE2 GLN A  73 " =    3.387
peak=    3.281 closest distance to " O   HOH Z  66 " =    2.070
peak=    3.280 closest distance to " NZ  LYS A 117 " =    1.113
peak=    3.279 closest distance to " O   HOH Z 145 " =    1.311
peak=    3.275 closest distance to " O   HOH Z 326 " =    1.389
peak=    3.275 closest distance to " O   HOH Z 115 " =    1.885
peak=    3.272 closest distance to " CB  MET A  47 " =    1.059
peak=    3.270 closest distance to " CB  LEU A 300 " =    0.999
peak=    3.269 closest distance to " CA  ILE A 234 " =    1.002
peak=    3.269 closest distance to " O   HOH Z 234 " =    3.890
peak=    3.268 closest distance to " CB  LEU A 143 " =    1.068
peak=    3.255 closest distance to " O   HOH Z  92 " =    1.029
peak=    3.253 closest distance to " O   HOH Z 214 " =    1.572
peak=    3.252 closest distance to " OG  SER A  22 " =    2.727
peak=    3.246 closest distance to " NH1BARG A 145 " =    1.165
peak=    3.241 closest distance to " CB  ASN A 187 " =    1.024
peak=    3.240 closest distance to " CB  GLU A 236 " =    1.276
peak=    3.239 closest distance to " CB  ALA A  21 " =    1.807
peak=    3.239 closest distance to " O   HOH Z 245 " =    1.236
peak=    3.238 closest distance to " CB  VAL A 265 " =    2.068
peak=    3.228 closest distance to " OG  SER A 206 " =    1.201
peak=    3.228 closest distance to " CB  ALA A 291 " =    3.384
peak=    3.227 closest distance to " O   HOH Z 345 " =    3.377
peak=    3.223 closest distance to " O   HOH Z 430 " =    1.522
peak=    3.223 closest distance to " CG2BVAL A  41 " =    0.922
peak=    3.220 closest distance to " O   HOH Z 425 " =    1.985
peak=    3.220 closest distance to " CG  GLU A   2 " =    1.153
peak=    3.219 closest distance to " O   ASN A 209 " =    1.301
peak=    3.219 closest distance to " CA  SER A  87 " =    0.944
peak=    3.217 closest distance to " O   HOH Z 211 " =    1.307
peak=    3.213 closest distance to " NE2 GLN A  58 " =    5.731
peak=    3.213 closest distance to " O   ALA A 165 " =    1.333
peak=    3.211 closest distance to " N   ASN A 127 " =    1.298
peak=    3.207 closest distance to " CB  LYS A 117 " =    1.173
peak=    3.207 closest distance to " O   HOH Z 269 " =    1.161
peak=    3.198 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.198 closest distance to " O   HOH Z 158 " =    2.888
peak=    3.189 closest distance to " O   HOH Z 250 " =    1.609
peak=    3.188 closest distance to " CB  ALA A  43 " =    0.984
peak=    3.186 closest distance to " CD1 ILE A  33 " =    1.581
peak=    3.185 closest distance to " OG BSER A 164 " =    2.558
peak=    3.181 closest distance to " OE2 GLU A  53 " =    2.173
peak=    3.181 closest distance to " CZ AARG A 102 " =    1.918
peak=    3.180 closest distance to " CB  PRO A 243 " =    1.222
peak=    3.178 closest distance to " N   CYS A 260 " =    0.721
peak=    3.175 closest distance to " CD  PRO A 243 " =    1.778
peak=    3.175 closest distance to " O   GLY A 147 " =    1.478
peak=    3.172 closest distance to " CA  ALA A  43 " =    1.311
peak=    3.170 closest distance to " O   HOH Z 389 " =    1.736
peak=    3.168 closest distance to " OD2 ASP A  65 " =    2.359
peak=    3.166 closest distance to " O   ALA A  10 " =    1.607
peak=    3.165 closest distance to " O   HOH Z  89 " =    1.554
peak=    3.164 closest distance to " N   GLY A 196 " =    1.010
peak=    3.163 closest distance to " O   HOH Z 409 " =    3.457
peak=    3.162 closest distance to " O   HOH Z 116 " =    1.675
peak=    3.160 closest distance to " OD1 ASN A 217 " =    1.562
peak=    3.155 closest distance to " CG2 VAL A 174 " =    1.343
peak=    3.153 closest distance to " O   HOH Z 225 " =    1.978
peak=    3.149 closest distance to " OD1 ASP A 238 " =    1.041
peak=    3.143 closest distance to " O   HOH Z 181 " =    2.153
peak=    3.141 closest distance to " CD BARG A 102 " =    1.173
peak=    3.140 closest distance to " O   HOH Z 156 " =    2.836
peak=    3.139 closest distance to " CE BMET A  47 " =    1.385
peak=    3.138 closest distance to " CA  ALA A 233 " =    1.219
peak=    3.128 closest distance to " CA  VAL A 126 " =    1.110
peak=    3.124 closest distance to " O   HOH Z 387 " =    3.042
peak=    3.123 closest distance to " O   HOH Z 407 " =    1.902
peak=    3.122 closest distance to " O   HOH Z 220 " =    1.283
peak=    3.118 closest distance to " O   HOH Z  63 " =    2.481
peak=    3.116 closest distance to " O   GLY A  57 " =    2.452
peak=    3.105 closest distance to " CG1BVAL A  72 " =    1.396
peak=    3.101 closest distance to " O   HOH Z 287 " =    2.018
peak=    3.101 closest distance to " O   HOH Z 343 " =    1.274
peak=    3.099 closest distance to " O   TYR A 116 " =    1.397
peak=    3.085 closest distance to " CA  PHE A 208 " =    0.967
peak=    3.074 closest distance to " CA  LEU A 101 " =    1.450
peak=    3.071 closest distance to " O   HOH Z 365 " =    5.703
peak=    3.062 closest distance to " O   HOH Z   1 " =    1.519
peak=    3.061 closest distance to " CA  PRO A  54 " =    1.273
peak=    3.058 closest distance to " NH2BARG A 145 " =    1.197
peak=    3.048 closest distance to " CB  ARG A 138 " =    0.954
peak=    3.042 closest distance to " O   HOH Z 263 " =    1.526
peak=    3.018 closest distance to " O   HOH Z 128 " =    2.068
peak=    3.009 closest distance to " O   HOH Z   9 " =    1.616

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.754 - 5.795
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.754 - 5.795

peak=   -4.789 closest distance to " O   HOH Z 377 " =    1.747
peak=   -4.580 closest distance to " CD  ARG A  14 " =    3.333
peak=   -4.377 closest distance to " CB  PRO A 243 " =    2.525
peak=   -4.312 closest distance to " O   PRO A 198 " =    1.319
peak=   -4.279 closest distance to " O   HOH Z  98 " =    1.865
peak=   -4.241 closest distance to " O   HOH Z 166 " =    1.182
peak=   -4.146 closest distance to " O   HOH Z 290 " =    1.048
peak=   -4.143 closest distance to " O   HOH Z 198 " =    2.113
peak=   -4.086 closest distance to " CG  MET A 105 " =    0.935
peak=   -4.074 closest distance to " O   HOH Z 407 " =    3.323
peak=   -4.032 closest distance to " N   GLN A  58 " =    1.774
peak=   -4.031 closest distance to " CD  ARG A 156 " =    1.942
peak=   -4.029 closest distance to " CD  GLN A  88 " =    0.855
peak=   -4.027 closest distance to " ND2 ASN A  45 " =    0.934
peak=   -4.026 closest distance to " O   HOH Z 102 " =    1.773
peak=   -4.010 closest distance to " O   HOH Z 266 " =    4.361
peak=   -3.953 closest distance to " C   ASN A 285 " =    2.371
peak=   -3.927 closest distance to " CB  CYS A 201 " =    2.355
peak=   -3.916 closest distance to " O   HOH Z  13 " =    1.293
peak=   -3.915 closest distance to " C   HIS A 108 " =    1.148
peak=   -3.911 closest distance to " C   ALA A 158 " =    1.251
peak=   -3.905 closest distance to " CA  VAL A 153 " =    2.417
peak=   -3.904 closest distance to " O   HOH Z 231 " =    1.723
peak=   -3.904 closest distance to " CB  TYR A  15 " =    2.146
peak=   -3.883 closest distance to " O   HOH Z 388 " =    1.904
peak=   -3.848 closest distance to " OE1 GLN A  88 " =    1.066
peak=   -3.819 closest distance to " CB  ALA A 291 " =    2.207
peak=   -3.807 closest distance to " CZ  PHE A  59 " =    1.582
peak=   -3.784 closest distance to " OG ASER A 134 " =    1.099
peak=   -3.772 closest distance to " O   HOH Z  43 " =    1.694
peak=   -3.758 closest distance to " O   ALA A 161 " =    1.623
peak=   -3.752 closest distance to " CE2 TYR A  30 " =    2.814
peak=   -3.740 closest distance to " CB  PHE A 283 " =    2.619
peak=   -3.738 closest distance to " O   HOH Z 438 " =    0.953
peak=   -3.732 closest distance to " O   HOH Z  93 " =    2.106
peak=   -3.730 closest distance to " CG  GLN A 223 " =    2.007
peak=   -3.707 closest distance to " OG1 THR A   4 " =    1.925
peak=   -3.700 closest distance to " O   HOH Z 185 " =    2.153
peak=   -3.697 closest distance to " O   HOH Z 385 " =    1.955
peak=   -3.688 closest distance to " OD1 ASP A 191 " =    1.877
peak=   -3.676 closest distance to " CG  LYS A 193 " =    2.285
peak=   -3.672 closest distance to " CB  ALA A   7 " =    2.006
peak=   -3.660 closest distance to " O   SER A 135 " =    1.503
peak=   -3.657 closest distance to " O   HOH Z 213 " =    1.203
peak=   -3.650 closest distance to " CB  ALA A 248 " =    1.880
peak=   -3.647 closest distance to " OG BSER A 134 " =    1.178
peak=   -3.638 closest distance to " O   HOH Z 435 " =    2.846
peak=   -3.637 closest distance to " OXT GLY A 302 " =    2.954
peak=   -3.626 closest distance to " CB  ASP A  27 " =    2.370
peak=   -3.625 closest distance to " O   HOH Z 298 " =    1.167
peak=   -3.622 closest distance to " O   PRO A 163 " =    1.742
peak=   -3.622 closest distance to " OG  SER A  97 " =    2.048
peak=   -3.615 closest distance to " O   VAL A  67 " =    2.663
peak=   -3.603 closest distance to " O   GLY A 211 " =    1.386
peak=   -3.599 closest distance to " O   TRP A  70 " =    1.501
peak=   -3.597 closest distance to " O   HOH Z 250 " =    1.529
peak=   -3.595 closest distance to " NE BARG A 102 " =    2.381
peak=   -3.587 closest distance to " OD1 ASN A 187 " =    1.535
peak=   -3.577 closest distance to " O   HOH Z  28 " =    1.914
peak=   -3.577 closest distance to " N   HIS A 115 " =    2.051
peak=   -3.571 closest distance to " N   GLN A  88 " =    1.771
peak=   -3.565 closest distance to " OG  SER A 245 " =    1.069
peak=   -3.545 closest distance to " O   ALA A  51 " =    1.431
peak=   -3.527 closest distance to " CE  MET A  93 " =    1.111
peak=   -3.519 closest distance to " ND2 ASN A  60 " =    1.484
peak=   -3.509 closest distance to " O   HOH Z  60 " =    1.722
peak=   -3.505 closest distance to " O   SER A 146 " =    0.917
peak=   -3.492 closest distance to " CE2 PHE A 218 " =    2.497
peak=   -3.488 closest distance to " CB  ALA A  43 " =    2.325
peak=   -3.487 closest distance to " CG  ASP A 231 " =    0.754
peak=   -3.475 closest distance to " CB  CYS A 254 " =    2.215
peak=   -3.471 closest distance to " O   ILE A  49 " =    1.531
peak=   -3.464 closest distance to " O   HOH Z 152 " =    4.996
peak=   -3.462 closest distance to " O   HOH Z 124 " =    1.130
peak=   -3.460 closest distance to " O   HOH Z 377 " =    1.028
peak=   -3.458 closest distance to " CB  ASN A  39 " =    2.211
peak=   -3.444 closest distance to " CA  SER A 146 " =    2.288
peak=   -3.443 closest distance to " O   SER A  22 " =    2.507
peak=   -3.439 closest distance to " O   HOH Z  71 " =    0.969
peak=   -3.437 closest distance to " N   ARG A  14 " =    1.025
peak=   -3.437 closest distance to " O   HOH Z 137 " =    1.371
peak=   -3.433 closest distance to " CD  ARG A 139 " =    1.728
peak=   -3.426 closest distance to " C   LEU A 143 " =    1.336
peak=   -3.414 closest distance to " N   VAL A  72 " =    1.414
peak=   -3.412 closest distance to " O   HOH Z 409 " =    5.795
peak=   -3.408 closest distance to " CB  PRO A 163 " =    2.499
peak=   -3.406 closest distance to " N   GLN A 122 " =    1.468
peak=   -3.404 closest distance to " CZ3 TRP A 179 " =    1.301
peak=   -3.399 closest distance to " CB  SER A 245 " =    2.372
peak=   -3.398 closest distance to " CD1 LEU A 101 " =    2.347
peak=   -3.393 closest distance to " CG  PRO A 163 " =    2.433
peak=   -3.392 closest distance to " OE1 GLN A  77 " =    1.987
peak=   -3.391 closest distance to " CA  GLY A 241 " =    2.174
peak=   -3.372 closest distance to " NH2 ARG A  79 " =    1.841
peak=   -3.371 closest distance to " O   HOH Z 389 " =    1.839
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.213
peak=   -3.367 closest distance to " O   ILE A 109 " =    2.589
peak=   -3.367 closest distance to " CE  MET A 105 " =    2.154
peak=   -3.360 closest distance to " O   HOH Z 111 " =    0.988
peak=   -3.358 closest distance to " CA  GLY A 133 " =    1.902
peak=   -3.351 closest distance to " CE3 TRP A 274 " =    2.466
peak=   -3.351 closest distance to " O   HOH Z 351 " =    1.609
peak=   -3.343 closest distance to " O   VAL A 197 " =    1.345
peak=   -3.338 closest distance to " O   HOH Z  51 " =    1.050
peak=   -3.332 closest distance to " CD2 LEU A 237 " =    2.416
peak=   -3.327 closest distance to " CB  PRO A  90 " =    1.468
peak=   -3.325 closest distance to " O   HOH Z 210 " =    1.024
peak=   -3.323 closest distance to " N   MET A 188 " =    1.817
peak=   -3.322 closest distance to " O   HOH Z 313 " =    1.990
peak=   -3.319 closest distance to " O   HOH Z  97 " =    0.858
peak=   -3.314 closest distance to " O   HOH Z 410 " =    2.190
peak=   -3.314 closest distance to " N   GLN A  58 " =    1.400
peak=   -3.314 closest distance to " CG1 VAL A 197 " =    2.170
peak=   -3.314 closest distance to " N   ALA A  43 " =    2.301
peak=   -3.310 closest distance to " O   HOH Z 143 " =    2.306
peak=   -3.309 closest distance to " O   SER A  62 " =    2.126
peak=   -3.306 closest distance to " O   VAL A 189 " =    2.425
peak=   -3.305 closest distance to " OE1 GLN A  58 " =    2.839
peak=   -3.296 closest distance to " N   THR A 157 " =    1.552
peak=   -3.295 closest distance to " CZ BARG A 275 " =    1.951
peak=   -3.295 closest distance to " O   HOH Z  47 " =    1.529
peak=   -3.290 closest distance to " OG  SER A  87 " =    1.253
peak=   -3.284 closest distance to " O   MET A  40 " =    2.728
peak=   -3.282 closest distance to " CG  GLU A 152 " =    2.286
peak=   -3.277 closest distance to " O   HOH Z  63 " =    1.633
peak=   -3.275 closest distance to " O   PRO A 198 " =    1.219
peak=   -3.272 closest distance to " O   HOH Z 140 " =    4.703
peak=   -3.267 closest distance to " CE2 TYR A 116 " =    3.038
peak=   -3.261 closest distance to " CB  ALA A 131 " =    1.928
peak=   -3.259 closest distance to " O   HOH Z  25 " =    2.167
peak=   -3.258 closest distance to " O   ALA A   1 " =    1.146
peak=   -3.257 closest distance to " CE3 TRP A 123 " =    1.367
peak=   -3.256 closest distance to " OH  TYR A 214 " =    1.241
peak=   -3.254 closest distance to " N   SER A 276 " =    1.138
peak=   -3.247 closest distance to " O   HOH Z 234 " =    4.082
peak=   -3.246 closest distance to " CD1 PHE A  59 " =    1.893
peak=   -3.244 closest distance to " OD1 ASN A 148 " =    1.739
peak=   -3.244 closest distance to " O   HOH Z 393 " =    3.458
peak=   -3.244 closest distance to " O   HOH Z 281 " =    3.265
peak=   -3.242 closest distance to " O   PRO A 163 " =    1.129
peak=   -3.230 closest distance to " O   HOH Z  24 " =    1.273
peak=   -3.229 closest distance to " O   HOH Z  52 " =    1.541
peak=   -3.228 closest distance to " CD2 TYR A 293 " =    1.947
peak=   -3.228 closest distance to " CB  ILE A  33 " =    2.845
peak=   -3.226 closest distance to " O   HOH Z 385 " =    2.020
peak=   -3.225 closest distance to " O   HOH Z 426 " =    2.294
peak=   -3.224 closest distance to " NH1AARG A 275 " =    1.797
peak=   -3.224 closest distance to " O   HOH Z 193 " =    1.620
peak=   -3.222 closest distance to " OD2 ASP A 171 " =    2.110
peak=   -3.222 closest distance to " O   HOH Z 427 " =    1.377
peak=   -3.210 closest distance to " O   HOH Z 418 " =    1.526
peak=   -3.210 closest distance to " CD1 LEU A 228 " =    2.256
peak=   -3.209 closest distance to " CB  ALA A  51 " =    1.787
peak=   -3.204 closest distance to " O   PRO A 243 " =    2.425
peak=   -3.191 closest distance to " O   HOH Z 436 " =    1.062
peak=   -3.191 closest distance to " O   HOH Z  44 " =    2.080
peak=   -3.189 closest distance to " O   HOH Z 222 " =    0.972
peak=   -3.181 closest distance to " O   HOH Z  90 " =    1.697
peak=   -3.179 closest distance to " CG1BVAL A  41 " =    2.908
peak=   -3.178 closest distance to " OE2 GLU A 152 " =    0.966
peak=   -3.177 closest distance to " CZ  TYR A 169 " =    1.773
peak=   -3.173 closest distance to " NH2AARG A 275 " =    5.464
peak=   -3.167 closest distance to " O   HOH Z   1 " =    1.271
peak=   -3.160 closest distance to " O   TYR A 247 " =    2.762
peak=   -3.159 closest distance to " O   HOH Z 247 " =    1.697
peak=   -3.154 closest distance to " OG  SER A  26 " =    1.046
peak=   -3.152 closest distance to " ND2 ASN A  69 " =    1.389
peak=   -3.150 closest distance to " O   HOH Z 207 " =    1.903
peak=   -3.149 closest distance to " O   ALA A 100 " =    2.458
peak=   -3.148 closest distance to " OD2 ASP A 171 " =    1.650
peak=   -3.145 closest distance to " O   HOH Z  39 " =    1.529
peak=   -3.145 closest distance to " CB  PRO A 163 " =    2.414
peak=   -3.143 closest distance to " CE2 PHE A 204 " =    1.944
peak=   -3.141 closest distance to " OG  SER A 206 " =    1.918
peak=   -3.140 closest distance to " O   HOH Z  88 " =    2.191
peak=   -3.136 closest distance to " O   HOH Z 319 " =    2.663
peak=   -3.127 closest distance to " O   GLY A  80 " =    2.381
peak=   -3.127 closest distance to " O   HOH Z 198 " =    1.633
peak=   -3.125 closest distance to " CE1 TYR A 169 " =    2.463
peak=   -3.125 closest distance to " CB  PHE A 192 " =    1.669
peak=   -3.125 closest distance to " O   VAL A  67 " =    2.650
peak=   -3.120 closest distance to " O   HOH Z 263 " =    2.917
peak=   -3.120 closest distance to " O   HOH Z 383 " =    1.062
peak=   -3.115 closest distance to " O   HOH Z 298 " =    2.494
peak=   -3.110 closest distance to " CD1 TRP A 274 " =    1.698
peak=   -3.106 closest distance to " O   PHE A 218 " =    1.261
peak=   -3.101 closest distance to " O   HOH Z 348 " =    1.865
peak=   -3.099 closest distance to " CE  MET A 113 " =    2.291
peak=   -3.093 closest distance to " O   HOH Z 417 " =    2.641
peak=   -3.093 closest distance to " CG  GLU A 152 " =    1.538
peak=   -3.086 closest distance to " CB  ASP A 132 " =    2.069
peak=   -3.074 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.074 closest distance to " O   HOH Z 150 " =    1.395
peak=   -3.061 closest distance to " ND2 ASN A 249 " =    2.155
peak=   -3.051 closest distance to " O   HOH Z 211 " =    1.199
peak=   -3.034 closest distance to " O   HOH Z 222 " =    3.056
peak=   -2.970 closest distance to " OG1 THR A 246 " =    1.132

================= 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    :  0.4580 0.4619   6.265101e+00   6.264810e+00
   1_bss:  0.4485 0.4537   6.261911e+00   6.251575e+00
   1_xyz:  0.3376 0.3652   6.060615e+00   6.123947e+00
   1_adp:  0.3073 0.3745   6.008142e+00   6.137740e+00
   1_occ:  0.3069 0.3752   6.007570e+00   6.137158e+00
   2_bss:  0.3062 0.3743   6.008363e+00   6.134701e+00
   2_xyz:  0.2298 0.2930   5.771664e+00   5.946542e+00
   2_adp:  0.2104 0.2724   5.701428e+00   5.884422e+00
   2_occ:  0.2101 0.2720   5.700107e+00   5.883054e+00
   3_bss:  0.2098 0.2711   5.697851e+00   5.881760e+00
   3_xyz:  0.1597 0.2080   5.442340e+00   5.652241e+00
   3_adp:  0.1518 0.2006   5.400284e+00   5.618703e+00
   3_occ:  0.1516 0.2002   5.398918e+00   5.617014e+00
   4_bss:  0.1515 0.2002   5.398270e+00   5.616157e+00
   4_xyz:  0.1320 0.1775   5.272807e+00   5.502216e+00
   4_adp:  0.1218 0.1671   5.206137e+00   5.443271e+00
   4_occ:  0.1217 0.1670   5.205431e+00   5.442704e+00
   5_bss:  0.1217 0.1670   5.204965e+00   5.442630e+00
   5_xyz:  0.1159 0.1625   5.169710e+00   5.414786e+00
   5_adp:  0.1144 0.1603   5.156481e+00   5.400781e+00
   5_occ:  0.1143 0.1601   5.155865e+00   5.400291e+00
   5_bss:  0.1147 0.1597   5.156349e+00   5.400223e+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:  0.300  20.000  -1.959   0.562   2.170   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -1.959   0.562   2.170   0.000   0.000   0.000
   1_adp:  0.300  20.000  -1.959   0.562   2.170   0.000   0.000   0.000
   1_occ:  0.300  20.000  -1.959   0.562   2.170   0.000   0.000   0.000
   2_bss:  0.333  44.563  -1.407  -0.826   0.596  -0.000   0.000   0.000
   2_xyz:  0.333  44.563  -1.407  -0.826   0.596  -0.000   0.000   0.000
   2_adp:  0.333  44.563  -1.407  -0.826   0.596  -0.000   0.000   0.000
   2_occ:  0.333  44.563  -1.407  -0.826   0.596  -0.000   0.000   0.000
   3_bss:  0.333  42.499  -1.671  -1.919  -0.712  -0.000  -0.000  -0.000
   3_xyz:  0.333  42.499  -1.671  -1.919  -0.712  -0.000  -0.000  -0.000
   3_adp:  0.333  42.499  -1.671  -1.919  -0.712  -0.000  -0.000  -0.000
   3_occ:  0.333  42.499  -1.671  -1.919  -0.712  -0.000  -0.000  -0.000
   4_bss:  0.320  42.499  -2.352  -2.650  -1.685  -0.000  -0.000  -0.000
   4_xyz:  0.320  42.499  -2.352  -2.650  -1.685  -0.000  -0.000  -0.000
   4_adp:  0.320  42.499  -2.352  -2.650  -1.685  -0.000  -0.000  -0.000
   4_occ:  0.320  42.499  -2.352  -2.650  -1.685  -0.000  -0.000  -0.000
   5_bss:  0.316  43.179  -2.385  -2.738  -1.955  -0.000  -0.000  -0.000
   5_xyz:  0.316  43.179  -2.385  -2.738  -1.955  -0.000  -0.000  -0.000
   5_adp:  0.316  43.179  -2.385  -2.738  -1.955  -0.000  -0.000  -0.000
   5_occ:  0.316  43.179  -2.385  -2.738  -1.955  -0.000  -0.000  -0.000
   5_bss:  0.317  43.476  -2.276  -2.654  -1.943  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.072 0.4436  0.6075    67098.126
   1_bss:  54.576 0.4608  0.6382    63039.347
   1_xyz:  39.724 0.6463  0.8618    38448.201
   1_adp:  40.920 0.6308  0.8472    39565.047
   1_occ:  40.961 0.6302  0.8454    39543.054
   2_bss:  40.786 0.6323  0.8279    39380.825
   2_xyz:  30.455 0.7517  0.9581    22712.921
   2_adp:  27.352 0.7868  0.9769    19485.359
   2_occ:  27.315 0.7872  0.9763    19404.674
   3_bss:  27.181 0.7884  0.9462    19219.780
   3_xyz:  20.204 0.8594  0.9964    11183.226
   3_adp:  19.177 0.8697  1.0059    10451.304
   3_occ:  19.129 0.8702  1.0059    10402.973
   4_bss:  19.085 0.8704  0.9769    10362.651
   4_xyz:  16.304 0.8953  0.9898     7870.932
   4_adp:  14.996 0.9068  0.9905     7006.650
   4_occ:  14.969 0.9070  0.9905     6991.695
   5_bss:  14.962 0.9070  0.9858     6991.380
   5_xyz:  14.407 0.9115  0.9868     6551.313
   5_adp:  14.069 0.9145  0.9834     6404.791
   5_occ:  14.049 0.9147  0.9833     6391.638
   5_bss:  14.079 0.9144  0.9841     6399.090
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8003e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8003e-01
   1_xyz:   1.448  0.011  0.092 15.928  0.006  4.105   1.1675e-01
   1_adp:   1.448  0.011  0.092 15.928  0.006  4.105   1.1675e-01
   1_occ:   1.448  0.011  0.092 15.928  0.006  4.105   1.1675e-01
   2_bss:   1.448  0.011  0.092 15.928  0.006  4.105   1.1675e-01
   2_xyz:   1.296  0.008  0.080 14.699  0.006  4.107   8.2271e-02
   2_adp:   1.296  0.008  0.080 14.699  0.006  4.107   8.2271e-02
   2_occ:   1.296  0.008  0.080 14.699  0.006  4.107   8.2271e-02
   3_bss:   1.296  0.008  0.080 14.699  0.006  4.107   8.2271e-02
   3_xyz:   0.986  0.006  0.066 14.235  0.004  4.112   5.6967e-02
   3_adp:   0.986  0.006  0.066 14.235  0.004  4.112   5.6967e-02
   3_occ:   0.986  0.006  0.066 14.235  0.004  4.112   5.6967e-02
   4_bss:   0.986  0.006  0.066 14.235  0.004  4.112   5.6967e-02
   4_xyz:   0.997  0.006  0.069 14.359  0.004  4.110   5.6564e-02
   4_adp:   0.997  0.006  0.069 14.359  0.004  4.110   5.6564e-02
   4_occ:   0.997  0.006  0.069 14.359  0.004  4.110   5.6564e-02
   5_bss:   0.997  0.006  0.069 14.359  0.004  4.110   5.6564e-02
   5_xyz:   0.943  0.006  0.067 14.361  0.004  4.110   5.2633e-02
   5_adp:   0.943  0.006  0.067 14.361  0.004  4.110   5.2633e-02
   5_occ:   0.943  0.006  0.067 14.361  0.004  4.110   5.2633e-02
   5_bss:   0.943  0.006  0.067 14.361  0.004  4.110   5.2633e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.649   2.3881e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.649   2.3881e-01
   1_xyz:  10.404  0.065  0.409 86.475  0.029  2.088   9.9407e-02
   1_adp:  10.404  0.065  0.409 86.475  0.029  2.088   9.9407e-02
   1_occ:  10.404  0.065  0.409 86.475  0.029  2.088   9.9407e-02
   2_bss:  10.404  0.065  0.409 86.475  0.029  2.088   9.9407e-02
   2_xyz:   8.093  0.042  0.263 84.878  0.046  2.316   7.3985e-02
   2_adp:   8.093  0.042  0.263 84.878  0.046  2.316   7.3985e-02
   2_occ:   8.093  0.042  0.263 84.878  0.046  2.316   7.3985e-02
   3_bss:   8.093  0.042  0.263 84.878  0.046  2.316   7.3985e-02
   3_xyz:   7.275  0.036  0.313 81.260  0.035  2.343   6.6411e-02
   3_adp:   7.275  0.036  0.313 81.260  0.035  2.343   6.6411e-02
   3_occ:   7.275  0.036  0.313 81.260  0.035  2.343   6.6411e-02
   4_bss:   7.275  0.036  0.313 81.260  0.035  2.343   6.6411e-02
   4_xyz:   7.672  0.054  0.236 83.562  0.032  2.309   3.9422e-02
   4_adp:   7.672  0.054  0.236 83.562  0.032  2.309   3.9422e-02
   4_occ:   7.672  0.054  0.236 83.562  0.032  2.309   3.9422e-02
   5_bss:   7.672  0.054  0.236 83.562  0.032  2.309   3.9422e-02
   5_xyz:   7.265  0.045  0.203 85.156  0.031  2.313   3.6704e-02
   5_adp:   7.265  0.045  0.203 85.156  0.031  2.313   3.6704e-02
   5_occ:   7.265  0.045  0.203 85.156  0.031  2.313   3.6704e-02
   5_bss:   7.265  0.045  0.203 85.156  0.031  2.313   3.6704e-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:  89.50   0.00  18.75  89.50   0.00  14.98  88.90   0.00  39.28
   1_occ:  89.50   0.00  18.75  89.50   0.00  14.98  88.90   0.00  39.28
   2_bss:  89.50   0.00  18.75  89.50   0.00  14.98  88.90   0.00  39.28
   2_xyz:  89.50   0.00  18.75  89.50   0.00  14.98  88.90   0.00  39.28
   2_adp:  84.87   0.00  17.66  83.99   0.00  13.65  84.87   3.27  39.52
   2_occ:  84.87   0.00  17.66  83.99   0.00  13.65  84.87   3.27  39.52
   3_bss:  84.87   0.00  17.66  83.99   0.00  13.65  84.87   3.27  39.52
   3_xyz:  84.87   0.00  17.66  83.99   0.00  13.65  84.87   3.27  39.52
   3_adp:  84.59   0.00  17.65  83.81   0.00  13.60  84.59   5.08  39.72
   3_occ:  84.59   0.00  17.65  83.81   0.00  13.60  84.59   5.08  39.72
   4_bss:  84.59   0.00  17.65  83.81   0.00  13.60  84.59   5.08  39.72
   4_xyz:  84.59   0.00  17.65  83.81   0.00  13.60  84.59   5.08  39.72
   4_adp:  94.82   1.24  17.78  94.82   1.24  13.22  83.92   5.28  42.65
   4_occ:  94.82   1.24  17.78  94.82   1.24  13.22  83.92   5.28  42.65
   5_bss:  94.82   1.24  17.78  94.82   1.24  13.22  83.92   5.28  42.65
   5_xyz:  94.82   1.24  17.78  94.82   1.24  13.22  83.92   5.28  42.65
   5_adp:  99.82   1.36  17.52  99.82   1.36  13.06  90.50   6.26  41.75
   5_occ:  99.82   1.36  17.52  99.82   1.36  13.06  90.50   6.26  41.75
   5_bss:  99.77   1.31  17.47  99.77   1.31  13.02  90.45   6.22  41.70
------------------------------------------------------------------------
 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:    1.872    0.022    0.339
   1_adp:    1.872    0.022    0.339
   1_occ:    1.872    0.022    0.339
   2_bss:    1.872    0.022    0.339
   2_xyz:    1.382    0.045    0.535
   2_adp:    1.382    0.045    0.535
   2_occ:    1.382    0.045    0.535
   3_bss:    1.382    0.045    0.535
   3_xyz:    1.297    0.024    0.648
   3_adp:    1.297    0.024    0.648
   3_occ:    1.297    0.024    0.648
   4_bss:    1.297    0.024    0.648
   4_xyz:    1.279    0.011    0.693
   4_adp:    1.279    0.011    0.693
   4_occ:    1.279    0.011    0.693
   5_bss:    1.279    0.011    0.693
   5_xyz:    1.324    0.089    0.714
   5_adp:    1.324    0.089    0.714
   5_occ:    1.324    0.089    0.714
   5_bss:    1.324    0.089    0.714
------------------------------------------------------------------------

CPU time actual refinement: 368.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/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_869/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_869/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.41 
  Macro-tasks:
    bulk solvent and scale       = 43.83  
    individual site refinement   = 156.24 
    weights calculation          = 30.49  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 237.25 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 121.23 
    alpha_beta                      = 8.01   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 129.50 
    fmodel                         = 7.33   
    r_factors                      = 0.29   
    phase_errors                   = 10.64  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 280.92 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.149 micro seconds
Total CPU time: 6.37 minutes
from_scatterers_fft:    662 calls, 120.93 s
gradients_fft:          607 calls, 115.89 s

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

# Date 2008-01-16 Time 05:52:35 PST -0800 (1200491555.47 s)
Start R-work = 0.4580, R-free = 0.4619 (no bulk solvent and anisotropic scale)
Final R-work = 0.1397, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4485, R-free = 0.4537
Final R-work = 0.1147, R-free = 0.1597