# Date 2008-01-16 Time 05:44:56 PST -0800 (1200491096.61 s)
#phil __OFF__

Command line arguments: "../862.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27198
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 862

-------------------------------------------------------------------------------
  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, 45.9914, 85.9581, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.96339
Completeness in resolution range: 0.947519
Completeness with d_max=infinity: 0.944731

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9634

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, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.96339
Completeness in resolution range: 0.947519
Completeness with d_max=infinity: 0.944731

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2024 [2175/2201]  1958   217  10.0%
  bin  2:  4.2024 -  3.3475 [2079/2099]  1873   206   9.9%
  bin  3:  3.3475 -  2.9279 [2069/2088]  1856   213  10.3%
  bin  4:  2.9279 -  2.6618 [2029/2059]  1827   202  10.0%
  bin  5:  2.6618 -  2.4719 [2036/2055]  1840   196   9.6%
  bin  6:  2.4719 -  2.3267 [2012/2037]  1801   211  10.5%
  bin  7:  2.3267 -  2.2106 [2015/2043]  1818   197   9.8%
  bin  8:  2.2106 -  2.1146 [1990/2026]  1794   196   9.8%
  bin  9:  2.1146 -  2.0334 [1995/2037]  1795   200  10.0%
  bin 10:  2.0334 -  1.9634 [1189/2029]  1068   121  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/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: 0.16 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 36
        2.42 -     3.04: 2224
        3.04 -     3.66: 4740
        3.66 -     4.28: 9112
        4.28 -     4.90: 12364
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.831 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.881 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28471 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_862/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/model_refine_001.geo

CPU time processing inputs: 9.37


============================ 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 45.9914 85.95805 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: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4082   r_free= 0.4069   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.217336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.6877 0.99   1410  158 0.3405 0.3426      6.4879      6.4868|
|  2:  4.6877 -  3.7394 0.99   1352  151 0.3399 0.3286      6.7032      6.6361|
|  3:  3.7394 -  3.2722 0.99   1332  141 0.3639 0.3447      6.5734      6.6296|
|  4:  3.2722 -  2.9755 0.99   1325  155 0.3904 0.4097       6.452      6.4536|
|  5:  2.9755 -  2.7637 0.99   1318  150 0.4348 0.4005         6.3      6.2826|
|  6:  2.7637 -  2.6016 0.99   1313  139 0.4303 0.4631      6.2128      6.1925|
|  7:  2.6016 -  2.4719 0.99   1304  140 0.4405 0.4380      6.1838      6.1416|
|  8:  2.4719 -  2.3647 0.98   1282  143 0.4528 0.4199      6.1187      6.1088|
|  9:  2.3647 -  2.2740 0.98   1273  155 0.4408 0.4799      6.0774      6.1332|
| 10:  2.2740 -  2.1958 1.00   1319  145 0.4542 0.4452      6.0474       6.013|
| 11:  2.1958 -  2.1273 0.98   1288  133 0.4489 0.4750      5.9876      6.0263|
| 12:  2.1273 -  2.0667 0.98   1266  143 0.4625 0.4686      5.9231      5.9885|
| 13:  2.0667 -  2.0124 0.98   1280  138 0.4652 0.4549      5.8433       5.766|
| 14:  2.0124 -  1.9634 0.44    568   68 0.5065 0.4936       5.853       5.829|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.6877  1410   158  0.74  30.79   0.84     0.79      59857.82|
|  2:  4.6877 -  3.7394  1352   151  0.77  29.34   0.93     0.87      79515.53|
|  3:  3.7394 -  3.2722  1332   141  0.68  36.75   0.96     0.87      84828.30|
|  4:  3.2722 -  2.9755  1325   155  0.61  42.77   0.96     0.81      79130.68|
|  5:  2.9755 -  2.7637  1318   150  0.53  49.19   0.92     0.74      64651.85|
|  6:  2.7637 -  2.6016  1313   139  0.53  49.89   0.93     0.72      56874.87|
|  7:  2.6016 -  2.4719  1304   140  0.52  50.88   0.96     0.71      50711.46|
|  8:  2.4719 -  2.3647  1282   143  0.50  52.24   0.94     0.70      46577.04|
|  9:  2.3647 -  2.2740  1273   155  0.51  51.36   0.97     0.70      41617.82|
| 10:  2.2740 -  2.1958  1319   145  0.51  51.37   0.98     0.73      38021.86|
| 11:  2.1958 -  2.1273  1288   133  0.49  53.05   1.01     0.73      37496.13|
| 12:  2.1273 -  2.0667  1266   143  0.46  55.21   0.98     0.70      34706.47|
| 13:  2.0667 -  2.0124  1280   138  0.44  57.20   0.98     0.68      30521.50|
| 14:  2.0124 -  1.9634   568    68  0.49  53.08   0.98     0.69      23910.08|
|alpha:            min =        0.68 max =            0.87 mean =         0.75|
|beta:             min =    23910.08 max =        84828.30 mean =     53515.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.91|
|phase err.(test): min =        0.00 max =           89.90 mean =        47.18|
|-----------------------------------------------------------------------------|

============================== 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 = 11.366592             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.147   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.602744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.079   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2026 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1889 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2851 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4666 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4446 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5628 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6736 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.324 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    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: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4082   r_free= 0.4069   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.217336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3962   r_free= 0.3986   ksol= 0.36   Bsol= 50.00   scale= 0.953   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.20,-1.74,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.203662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.993698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.229   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.827864              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.889   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3962      final r-factor (work) = 0.2672          |
| start r-factor (free) = 0.3986      final r-factor (free) = 0.3044          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.1722 = 9.99 * 0.50 * 6.2040 + 1.00 * 0.1716                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.2047 = 9.99 * 0.50 * 6.0211 + 1.00 * 0.1183                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2672      final r-factor (work) = 0.2443          |
| start r-factor (free) = 0.3044      final r-factor (free) = 0.3179          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9906 = 0.83 * 1.00 * 6.0211 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8395 = 0.83 * 1.00 * 5.8286 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.78   17.91    None  None   None       |
|    all(noH): 2823   0      0.00    97.78   17.91    None  None   None       |
|    Sol.    : 438    0      4.28    97.78   40.64    None  None   None       |
|    Mac.    : 2385   0      0.00    71.92   13.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.779:  934   |   5:    48.892 -  58.671:   99        |
|      1:     9.779 -  19.557: 1065   |   6:    58.671 -  68.449:   43        |
|      2:    19.557 -  29.335:  337   |   7:    68.449 -  78.228:   14        |
|      3:    29.335 -  39.114:  187   |   8:    78.228 -  88.006:    2        |
|      4:    39.114 -  48.892:  141   |   9:    88.006 -  97.785:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2443 r_free = 0.3179             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2440 r_free = 0.3175             target_work(ml) = 5.843         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2440   r_free= 0.3175   ksol= 0.36   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.20,-1.74,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.842693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2420   r_free= 0.3123   ksol= 0.34   Bsol= 57.92   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-0.37,-1.32,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.833165                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.910242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.467   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.228938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.403  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2420      final r-factor (work) = 0.1902          |
| start r-factor (free) = 0.3123      final r-factor (free) = 0.2432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5979 = 2.91 * 0.50 * 5.8274 + 1.00 * 0.1183                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4043 = 2.91 * 0.50 * 5.7371 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1803          |
| start r-factor (free) = 0.2432      final r-factor (free) = 0.2309          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3276 = 0.23 * 1.00 * 5.7371 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3490 = 0.23 * 1.00 * 5.5861 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.94   17.78    None  None   None       |
|    all(noH): 2823   0      0.00    96.94   17.78    None  None   None       |
|    Sol.    : 438    0      5.82    96.94   40.39    None  None   None       |
|    Mac.    : 2385   0      0.00    72.47   13.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.694:  871   |   5:    48.471 -  58.165:  100        |
|      1:     9.694 -  19.389: 1187   |   6:    58.165 -  67.860:   39        |
|      2:    19.389 -  29.083:  294   |   7:    67.860 -  77.554:   16        |
|      3:    29.083 -  38.777:  178   |   8:    77.554 -  87.248:    1        |
|      4:    38.777 -  48.471:  136   |   9:    87.248 -  96.942:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1803 r_free = 0.2309             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1801 r_free = 0.2310             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1801   r_free= 0.2310   ksol= 0.34   Bsol= 57.92   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-0.37,-1.32,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.564151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1798   r_free= 0.2297   ksol= 0.33   Bsol= 50.24   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.68,-1.20,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.559923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.219668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.645  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.120362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.501   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1798      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2297      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2535 = 2.22 * 0.50 * 5.5842 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1052 = 2.22 * 0.50 * 5.4545 + 1.00 * 0.0516                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1902      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1364 = 1.12 * 1.00 * 5.4545 + 1.00 * 0.0254                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9687 = 1.12 * 1.00 * 5.3178 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.54  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    100.54  18.07    None  None   None       |
|    Sol.    : 438    0      6.72    100.54  43.97    None  None   None       |
|    Mac.    : 2385   0      0.00    89.86   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.054: 1002   |   5:    50.268 -  60.322:  119        |
|      1:    10.054 -  20.107: 1133   |   6:    60.322 -  70.375:   45        |
|      2:    20.107 -  30.161:  239   |   7:    70.375 -  80.429:   35        |
|      3:    30.161 -  40.214:  143   |   8:    80.429 -  90.482:   10        |
|      4:    40.214 -  50.268:   96   |   9:    90.482 - 100.536:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1323 r_free = 0.1817             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1322 r_free = 0.1817             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1817   ksol= 0.33   Bsol= 50.24   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.68,-1.20,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.289469                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1817   ksol= 0.32   Bsol= 53.29   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.49,-1.47,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.288634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.254829              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.426  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.239858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.882  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0501 = 2.25 * 0.50 * 5.3206 + 1.00 * 0.0516                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9665 = 2.25 * 0.50 * 5.2437 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2685 = 0.24 * 1.00 * 5.2437 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2540 = 0.24 * 1.00 * 5.1918 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    96.49   17.43    None  None   None       |
|    all(noH): 2823   0      0.46    96.49   17.43    None  None   None       |
|    Sol.    : 438    0      6.49    96.49   41.60    None  None   None       |
|    Mac.    : 2385   0      0.46    90.94   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.459 -  10.062: 1035   |   5:    48.476 -  58.079:   97        |
|      1:    10.062 -  19.666: 1132   |   6:    58.079 -  67.683:   48        |
|      2:    19.666 -  29.269:  227   |   7:    67.683 -  77.286:   33        |
|      3:    29.269 -  38.872:  133   |   8:    77.286 -  86.889:   11        |
|      4:    38.872 -  48.476:  105   |   9:    86.889 -  96.493:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1615             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1616             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1616   ksol= 0.32   Bsol= 53.29   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.49,-1.47,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.172085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1615   ksol= 0.32   Bsol= 53.29   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.65,-1.43,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171773                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.965072              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.092  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.427188              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.549  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1556 = 1.97 * 0.50 * 5.1916 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1215 = 1.97 * 0.50 * 5.1576 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5272 = 2.43 * 1.00 * 5.1576 + 1.00 * 0.0087                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4852 = 2.43 * 1.00 * 5.1397 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.08  17.54    None  None   None       |
|    all(noH): 2823   0      0.00    101.08  17.54    None  None   None       |
|    Sol.    : 438    0      5.93    98.09   42.39    None  None   None       |
|    Mac.    : 2385   0      0.00    101.08  12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.108: 1065   |   5:    50.540 -  60.648:   88        |
|      1:    10.108 -  20.216: 1118   |   6:    60.648 -  70.756:   46        |
|      2:    20.216 -  30.324:  227   |   7:    70.756 -  80.864:   26        |
|      3:    30.324 -  40.432:  117   |   8:    80.864 -  90.972:    9        |
|      4:    40.432 -  50.540:  121   |   9:    90.972 - 101.080:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1577             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1578             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1578   ksol= 0.32   Bsol= 53.29   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.65,-1.43,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144579                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.6877 0.99   1410  158 0.0964 0.1288      5.3607      5.5639|
|  2:  4.6877 -  3.7394 0.99   1352  151 0.0849 0.1080      5.4382      5.6007|
|  3:  3.7394 -  3.2722 0.99   1332  141 0.1105 0.1562      5.4922        5.85|
|  4:  3.2722 -  2.9755 0.99   1325  155 0.1239 0.1701      5.4622       5.616|
|  5:  2.9755 -  2.7637 0.99   1318  150 0.1333 0.1724      5.3129      5.5421|
|  6:  2.7637 -  2.6016 0.99   1313  139 0.1184 0.1704      5.1915       5.399|
|  7:  2.6016 -  2.4719 0.99   1304  140 0.1258 0.1642      5.1552      5.3584|
|  8:  2.4719 -  2.3647 0.98   1282  143 0.1143 0.1806      5.0455      5.3654|
|  9:  2.3647 -  2.2740 0.98   1273  155 0.1157 0.1733      5.0286      5.3215|
| 10:  2.2740 -  2.1958 1.00   1319  145 0.1087 0.1635      4.9355      5.1527|
| 11:  2.1958 -  2.1273 0.98   1288  133 0.1125 0.1910      4.9516      5.3388|
| 12:  2.1273 -  2.0667 0.98   1266  143 0.1123 0.1625      4.8762      5.1256|
| 13:  2.0667 -  2.0124 0.98   1280  138 0.1111 0.1736      4.7858       5.038|
| 14:  2.0124 -  1.9634 0.44    568   68 0.0984 0.1535      4.6426      4.8772|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.6877  1410   158  0.94   8.76   0.98     0.95       6718.99|
|  2:  4.6877 -  3.7394  1352   151  0.95   7.81   1.02     1.01       8999.99|
|  3:  3.7394 -  3.2722  1332   141  0.93  11.46   1.03     1.03      10445.40|
|  4:  3.2722 -  2.9755  1325   155  0.92  13.90   1.01     0.99      10351.23|
|  5:  2.9755 -  2.7637  1318   150  0.90  15.65   1.00     0.98       7984.57|
|  6:  2.7637 -  2.6016  1313   139  0.90  15.65   0.99     0.97       6829.99|
|  7:  2.6016 -  2.4719  1304   140  0.91  15.47   1.00     0.96       6038.89|
|  8:  2.4719 -  2.3647  1282   143  0.91  15.21   0.98     0.96       5113.03|
|  9:  2.3647 -  2.2740  1273   155  0.91  15.38   1.00     0.97       4998.10|
| 10:  2.2740 -  2.1958  1319   145  0.90  15.45   1.00     0.96       4274.15|
| 11:  2.1958 -  2.1273  1288   133  0.90  16.21   0.99     0.95       4478.23|
| 12:  2.1273 -  2.0667  1266   143  0.91  15.91   1.01     1.00       4054.87|
| 13:  2.0667 -  2.0124  1280   138  0.90  16.17   1.00     0.98       3385.98|
| 14:  2.0124 -  1.9634   568    68  0.92  14.17   0.98     0.95       2525.06|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2525.06 max =        10445.40 mean =      6344.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1577   ksol= 0.32   Bsol= 53.29   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.58,-1.29,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1577   ksol= 0.32   Bsol= 53.29   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.58,-1.29,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.6877 0.99   1410  158 0.0964 0.1289      5.3614      5.5651|
|  2:  4.6877 -  3.7394 0.99   1352  151 0.0850 0.1080      5.4386      5.6008|
|  3:  3.7394 -  3.2722 0.99   1332  141 0.1105 0.1562      5.4923      5.8501|
|  4:  3.2722 -  2.9755 0.99   1325  155 0.1239 0.1701      5.4623      5.6159|
|  5:  2.9755 -  2.7637 0.99   1318  150 0.1333 0.1724      5.3127      5.5418|
|  6:  2.7637 -  2.6016 0.99   1313  139 0.1184 0.1703      5.1913      5.3986|
|  7:  2.6016 -  2.4719 0.99   1304  140 0.1258 0.1642      5.1552      5.3585|
|  8:  2.4719 -  2.3647 0.98   1282  143 0.1143 0.1806      5.0455      5.3652|
|  9:  2.3647 -  2.2740 0.98   1273  155 0.1158 0.1732      5.0286      5.3212|
| 10:  2.2740 -  2.1958 1.00   1319  145 0.1086 0.1637      4.9357      5.1538|
| 11:  2.1958 -  2.1273 0.98   1288  133 0.1125 0.1909      4.9517      5.3388|
| 12:  2.1273 -  2.0667 0.98   1266  143 0.1122 0.1623       4.876      5.1256|
| 13:  2.0667 -  2.0124 0.98   1280  138 0.1111 0.1735      4.7854      5.0373|
| 14:  2.0124 -  1.9634 0.44    568   68 0.0983 0.1532      4.6418      4.8758|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.6877  1410   158  0.94   8.78   0.98     0.95       6730.39|
|  2:  4.6877 -  3.7394  1352   151  0.95   7.81   1.02     1.01       9010.13|
|  3:  3.7394 -  3.2722  1332   141  0.93  11.46   1.04     1.03      10449.79|
|  4:  3.2722 -  2.9755  1325   155  0.92  13.90   1.02     0.99      10349.59|
|  5:  2.9755 -  2.7637  1318   150  0.90  15.65   1.00     0.98       7980.01|
|  6:  2.7637 -  2.6016  1313   139  0.90  15.65   0.99     0.98       6826.55|
|  7:  2.6016 -  2.4719  1304   140  0.91  15.47   1.00     0.97       6036.70|
|  8:  2.4719 -  2.3647  1282   143  0.91  15.21   0.99     0.96       5111.32|
|  9:  2.3647 -  2.2740  1273   155  0.91  15.38   1.01     0.97       4996.97|
| 10:  2.2740 -  2.1958  1319   145  0.90  15.46   1.00     0.97       4276.86|
| 11:  2.1958 -  2.1273  1288   133  0.90  16.22   1.00     0.95       4481.40|
| 12:  2.1273 -  2.0667  1266   143  0.91  15.91   1.01     1.01       4054.81|
| 13:  2.0667 -  2.0124  1280   138  0.90  16.16   1.00     0.98       3382.58|
| 14:  2.0124 -  1.9634   568    68  0.92  14.14   0.99     0.96       2520.21|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2520.21 max =        10449.79 mean =      6345.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.02|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.722)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.08  17.54    None  None   None       |
|    all(noH): 2823   0      0.00    101.08  17.54    None  None   None       |
|    Sol.    : 438    0      5.94    98.10   42.40    None  None   None       |
|    Mac.    : 2385   0      0.00    101.08  12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.111: 1065   |   5:    50.543 -  60.651:   88        |
|      1:    10.111 -  20.219: 1118   |   6:    60.651 -  70.759:   46        |
|      2:    20.219 -  30.327:  227   |   7:    70.759 -  80.867:   26        |
|      3:    30.327 -  40.435:  117   |   8:    80.867 -  90.975:    9        |
|      4:    40.435 -  50.543:  121   |   9:    90.975 - 101.083:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 4.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 297
   mapped sites are within: 0.706 - 4.628

peak=    6.644 closest distance to " NE2 GLN A  11 " =    1.312
peak=    5.669 closest distance to " O   HOH Z 126 " =    2.147
peak=    5.484 closest distance to " CG  PRO A  54 " =    1.268
peak=    5.414 closest distance to " NH2 ARG A  56 " =    2.085
peak=    5.236 closest distance to " O   HOH Z 144 " =    1.694
peak=    5.121 closest distance to " CB  GLN A 223 " =    1.495
peak=    5.105 closest distance to " O   HOH Z 427 " =    2.413
peak=    5.033 closest distance to " O   HOH Z 417 " =    1.531
peak=    4.967 closest distance to " O   HOH Z 423 " =    1.962
peak=    4.942 closest distance to " CB  SER A  63 " =    1.267
peak=    4.852 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.842 closest distance to " CG  PRO A 198 " =    1.247
peak=    4.840 closest distance to " O   HOH Z  63 " =    1.665
peak=    4.816 closest distance to " CG  PRO A 213 " =    1.306
peak=    4.809 closest distance to " O   HOH Z 287 " =    1.907
peak=    4.791 closest distance to " O   HOH Z   7 " =    1.367
peak=    4.720 closest distance to " O   HOH Z 236 " =    1.490
peak=    4.709 closest distance to " CB  PRO A  54 " =    0.985
peak=    4.704 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.644 closest distance to " O   HOH Z 369 " =    2.259
peak=    4.633 closest distance to " O   HOH Z 298 " =    2.044
peak=    4.613 closest distance to " O   HOH Z  78 " =    1.662
peak=    4.596 closest distance to " CA  TYR A  30 " =    1.014
peak=    4.548 closest distance to " CB  ASN A 148 " =    1.347
peak=    4.520 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.461 closest distance to " O   HOH Z 425 " =    1.418
peak=    4.426 closest distance to " O   HOH Z 380 " =    1.726
peak=    4.422 closest distance to " O   HOH Z   2 " =    1.661
peak=    4.420 closest distance to " CG  PRO A  90 " =    1.106
peak=    4.384 closest distance to " CB  GLU A 128 " =    1.018
peak=    4.305 closest distance to " O   HOH Z   1 " =    1.809
peak=    4.286 closest distance to " C   PRO A 198 " =    1.484
peak=    4.286 closest distance to " CD  ARG A 159 " =    0.822
peak=    4.254 closest distance to " O   HOH Z 209 " =    2.275
peak=    4.246 closest distance to " CG2 VAL A 257 " =    0.930
peak=    4.241 closest distance to " CB  GLU A 152 " =    1.380
peak=    4.240 closest distance to " CG  LEU A 167 " =    1.243
peak=    4.165 closest distance to " O   HOH Z  57 " =    2.332
peak=    4.161 closest distance to " OG ASER A 258 " =    3.102
peak=    4.154 closest distance to " ND2 ASN A 187 " =    1.468
peak=    4.153 closest distance to " O   HOH Z 193 " =    1.779
peak=    4.150 closest distance to " OG BSER A  99 " =    2.294
peak=    4.122 closest distance to " CB  SER A 216 " =    0.880
peak=    4.121 closest distance to " CB  ASN A 187 " =    1.171
peak=    4.110 closest distance to " CB  SER A   3 " =    1.390
peak=    4.076 closest distance to " O   HOH Z 132 " =    2.289
peak=    4.043 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.040 closest distance to " O   HOH Z 133 " =    2.433
peak=    4.026 closest distance to " O   HOH Z   1 " =    1.656
peak=    4.017 closest distance to " CG  TRP A 179 " =    2.222
peak=    4.005 closest distance to " O   HOH Z 217 " =    2.870
peak=    3.993 closest distance to " O   HOH Z   9 " =    2.075
peak=    3.993 closest distance to " ND1 HIS A  86 " =    1.764
peak=    3.984 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.981 closest distance to " O   HOH Z  61 " =    1.640
peak=    3.956 closest distance to " CB  ARG A 190 " =    1.691
peak=    3.945 closest distance to " CB  VAL A 265 " =    1.291
peak=    3.943 closest distance to " O   HOH Z 368 " =    3.662
peak=    3.943 closest distance to " O   HOH Z 394 " =    1.655
peak=    3.939 closest distance to " O   HOH Z 214 " =    2.009
peak=    3.927 closest distance to " CD  ARG A  66 " =    2.212
peak=    3.908 closest distance to " O   HOH Z 392 " =    1.255
peak=    3.907 closest distance to " O   HOH Z 158 " =    2.759
peak=    3.881 closest distance to " O   HOH Z 261 " =    1.673
peak=    3.879 closest distance to " O   HOH Z 250 " =    1.496
peak=    3.877 closest distance to " O   HOH Z 389 " =    1.852
peak=    3.875 closest distance to " N   PHE A 130 " =    1.219
peak=    3.868 closest distance to " O   HOH Z 437 " =    1.964
peak=    3.864 closest distance to " O   HOH Z  44 " =    1.714
peak=    3.855 closest distance to " O   HOH Z 171 " =    2.884
peak=    3.813 closest distance to " CD BLYS A 290 " =    1.044
peak=    3.804 closest distance to " CB  THR A 157 " =    1.148
peak=    3.800 closest distance to " CB  ARG A 139 " =    1.024
peak=    3.799 closest distance to " CB  ARG A  79 " =    1.292
peak=    3.798 closest distance to " CB  TRP A 266 " =    1.047
peak=    3.781 closest distance to " OD1 ASN A  69 " =    2.704
peak=    3.781 closest distance to " O   SER A  87 " =    2.287
peak=    3.777 closest distance to " CA  ASN A 215 " =    1.160
peak=    3.770 closest distance to " O   HOH Z 371 " =    2.032
peak=    3.766 closest distance to " CG2 THR A 221 " =    1.034
peak=    3.755 closest distance to " CB  GLU A 277 " =    3.555
peak=    3.751 closest distance to " CG1 ILE A  33 " =    1.212
peak=    3.740 closest distance to " O   HOH Z 116 " =    2.874
peak=    3.736 closest distance to " O   HOH Z  88 " =    3.171
peak=    3.730 closest distance to " CB  TYR A 169 " =    0.900
peak=    3.727 closest distance to " CA  ASP A 124 " =    0.706
peak=    3.727 closest distance to " O   HOH Z 352 " =    1.660
peak=    3.723 closest distance to " O   HOH Z 327 " =    1.676
peak=    3.713 closest distance to " O   HOH Z  40 " =    2.240
peak=    3.701 closest distance to " O   HOH Z 425 " =    2.003
peak=    3.697 closest distance to " CE  LYS A  76 " =    0.819
peak=    3.680 closest distance to " O   HOH Z 175 " =    2.144
peak=    3.679 closest distance to " CA  TYR A  30 " =    1.060
peak=    3.673 closest distance to " O   HOH Z 213 " =    2.106
peak=    3.663 closest distance to " O   HOH Z 405 " =    1.425
peak=    3.662 closest distance to " CE3 TRP A 274 " =    2.225
peak=    3.656 closest distance to " N   GLN A 278 " =    1.098
peak=    3.655 closest distance to " O   HOH Z 258 " =    2.193
peak=    3.655 closest distance to " CA  GLY A 241 " =    3.702
peak=    3.652 closest distance to " CB  TRP A 179 " =    1.439
peak=    3.650 closest distance to " NE AARG A 275 " =    1.397
peak=    3.643 closest distance to " O   HOH Z 146 " =    1.653
peak=    3.641 closest distance to " O   HOH Z 135 " =    1.624
peak=    3.641 closest distance to " CB  TYR A 116 " =    0.891
peak=    3.636 closest distance to " CA  ALA A 299 " =    0.885
peak=    3.632 closest distance to " CB  LYS A 117 " =    1.249
peak=    3.627 closest distance to " O   HOH Z  44 " =    2.836
peak=    3.620 closest distance to " O   HOH Z 234 " =    3.725
peak=    3.619 closest distance to " CG  PRO A 243 " =    1.102
peak=    3.614 closest distance to " O   HOH Z 193 " =    1.690
peak=    3.609 closest distance to " O   HOH Z  21 " =    1.686
peak=    3.602 closest distance to " O   HOH Z  61 " =    1.518
peak=    3.599 closest distance to " O   HOH Z 365 " =    2.739
peak=    3.598 closest distance to " O   HOH Z 115 " =    1.501
peak=    3.597 closest distance to " O   HOH Z  10 " =    1.770
peak=    3.588 closest distance to " OD2 ASP A 286 " =    2.738
peak=    3.585 closest distance to " CA  THR A 264 " =    0.859
peak=    3.582 closest distance to " CD2 LEU A 255 " =    1.563
peak=    3.577 closest distance to " O   HOH Z  59 " =    1.538
peak=    3.573 closest distance to " OG BSER A 164 " =    2.293
peak=    3.570 closest distance to " O   HOH Z  88 " =    3.916
peak=    3.568 closest distance to " CB  SER A 276 " =    1.119
peak=    3.567 closest distance to " CB  ILE A 120 " =    1.345
peak=    3.564 closest distance to " OG  SER A  62 " =    3.042
peak=    3.558 closest distance to " CB  ALA A  34 " =    1.199
peak=    3.556 closest distance to " CA  ILE A 234 " =    1.066
peak=    3.554 closest distance to " O   HOH Z 371 " =    2.806
peak=    3.554 closest distance to " NE2 GLN A  73 " =    3.668
peak=    3.553 closest distance to " O   HOH Z   3 " =    1.948
peak=    3.550 closest distance to " O   HOH Z 222 " =    2.450
peak=    3.544 closest distance to " N   TYR A  15 " =    0.898
peak=    3.544 closest distance to " CZ  PHE A 218 " =    1.040
peak=    3.535 closest distance to " O   HOH Z 180 " =    2.096
peak=    3.535 closest distance to " CA  SER A  87 " =    1.063
peak=    3.533 closest distance to " O   HOH Z 144 " =    2.339
peak=    3.527 closest distance to " O   HOH Z  97 " =    2.064
peak=    3.527 closest distance to " O   HOH Z 271 " =    2.465
peak=    3.523 closest distance to " O   HOH Z 195 " =    1.356
peak=    3.513 closest distance to " O   HOH Z   9 " =    1.199
peak=    3.512 closest distance to " N   SER A  97 " =    0.853
peak=    3.501 closest distance to " O   ASN A 209 " =    1.415
peak=    3.497 closest distance to " CB  LEU A 143 " =    1.097
peak=    3.484 closest distance to " O   HOH Z 108 " =    2.062
peak=    3.482 closest distance to " CG1 ILE A 151 " =    0.975
peak=    3.476 closest distance to " O   HOH Z  68 " =    2.128
peak=    3.476 closest distance to " O   HOH Z 403 " =    1.352
peak=    3.475 closest distance to " O   HOH Z 302 " =    1.569
peak=    3.474 closest distance to " O   HOH Z  17 " =    1.800
peak=    3.460 closest distance to " O   HOH Z 128 " =    2.170
peak=    3.451 closest distance to " O   HOH Z 362 " =    1.994
peak=    3.450 closest distance to " O   HOH Z 290 " =    0.956
peak=    3.448 closest distance to " O   HOH Z 286 " =    2.326
peak=    3.438 closest distance to " CA  ARG A 195 " =    1.377
peak=    3.436 closest distance to " N   GLU A   2 " =    1.343
peak=    3.431 closest distance to " CA  ALA A 233 " =    1.060
peak=    3.428 closest distance to " O   HOH Z 227 " =    1.837
peak=    3.422 closest distance to " CB  ALA A 114 " =    1.094
peak=    3.421 closest distance to " OE2 GLU A  53 " =    2.060
peak=    3.415 closest distance to " N   SER A 134 " =    1.361
peak=    3.410 closest distance to " O   HOH Z 289 " =    1.650
peak=    3.409 closest distance to " O   HOH Z 193 " =    2.102
peak=    3.406 closest distance to " O   HOH Z 386 " =    3.098
peak=    3.404 closest distance to " CE1 TYR A 186 " =    1.366
peak=    3.399 closest distance to " O   HOH Z 225 " =    1.467
peak=    3.398 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.397 closest distance to " O   HOH Z 368 " =    1.927
peak=    3.397 closest distance to " O   HOH Z 344 " =    3.162
peak=    3.396 closest distance to " OD1BASN A 224 " =    2.227
peak=    3.396 closest distance to " CB  TYR A 169 " =    0.882
peak=    3.395 closest distance to " N   ALA A 154 " =    0.845
peak=    3.394 closest distance to " O   HOH Z 130 " =    3.751
peak=    3.391 closest distance to " CA  LEU A 101 " =    1.648
peak=    3.387 closest distance to " O   HOH Z 272 " =    2.080
peak=    3.378 closest distance to " CA  GLY A 267 " =    1.266
peak=    3.375 closest distance to " CB  SER A 212 " =    1.136
peak=    3.370 closest distance to " CB  THR A  31 " =    1.742
peak=    3.366 closest distance to " N   ALA A   1 " =    1.984
peak=    3.364 closest distance to " CA  ARG A 102 " =    1.184
peak=    3.357 closest distance to " NH2BARG A 145 " =    2.103
peak=    3.356 closest distance to " CB  GLN A  88 " =    1.266
peak=    3.355 closest distance to " NH1AARG A 145 " =    1.202
peak=    3.353 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.352 closest distance to " O   HOH Z 207 " =    2.178
peak=    3.350 closest distance to " O   HOH Z 357 " =    1.938
peak=    3.349 closest distance to " N   ASN A 127 " =    1.346
peak=    3.344 closest distance to " CB  VAL A 202 " =    1.677
peak=    3.343 closest distance to " CB  SER A  62 " =    1.183
peak=    3.343 closest distance to " O   HOH Z 426 " =    1.887
peak=    3.334 closest distance to " O   HOH Z 172 " =    2.762
peak=    3.331 closest distance to " CD2 LEU A 297 " =    1.043
peak=    3.330 closest distance to " O   HOH Z  59 " =    2.047
peak=    3.324 closest distance to " O   HOH Z 219 " =    2.311
peak=    3.323 closest distance to " O   TYR A 116 " =    1.346
peak=    3.321 closest distance to " CB  ASN A 142 " =    0.922
peak=    3.319 closest distance to " NE2 GLN A  58 " =    3.652
peak=    3.318 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.316 closest distance to " O   HOH Z 119 " =    1.554
peak=    3.306 closest distance to " CD  PRO A 243 " =    1.788
peak=    3.306 closest distance to " O   HOH Z 343 " =    3.307
peak=    3.305 closest distance to " CG  GLU A 277 " =    1.954
peak=    3.305 closest distance to " N   ARG A 156 " =    1.280
peak=    3.304 closest distance to " OG  SER A  62 " =    2.984
peak=    3.302 closest distance to " O   HOH Z 281 " =    1.824
peak=    3.300 closest distance to " CB  ASP A 124 " =    0.876
peak=    3.298 closest distance to " O   HOH Z 189 " =    2.157
peak=    3.294 closest distance to " O   HOH Z 305 " =    3.616
peak=    3.284 closest distance to " NH1 ARG A  14 " =    0.979
peak=    3.282 closest distance to " CA  ALA A 160 " =    0.836
peak=    3.281 closest distance to " NZ  LYS A 117 " =    1.298
peak=    3.279 closest distance to " CD  LYS A 166 " =    1.362
peak=    3.278 closest distance to " O   HOH Z 207 " =    1.690
peak=    3.275 closest distance to " O   HOH Z  58 " =    1.573
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.758
peak=    3.274 closest distance to " O   HOH Z 390 " =    2.480
peak=    3.273 closest distance to " O   HOH Z  90 " =    2.205
peak=    3.271 closest distance to " O   HOH Z 139 " =    1.091
peak=    3.269 closest distance to " O   HOH Z 211 " =    2.658
peak=    3.268 closest distance to " O   HOH Z 122 " =    1.422
peak=    3.262 closest distance to " O   HOH Z 432 " =    1.884
peak=    3.259 closest distance to " NH2 ARG A 219 " =    1.780
peak=    3.254 closest distance to " O   HOH Z 313 " =    1.563
peak=    3.253 closest distance to " CA  ALA A 154 " =    0.965
peak=    3.252 closest distance to " CG2 ILE A 106 " =    0.938
peak=    3.251 closest distance to " O   HOH Z  43 " =    2.209
peak=    3.248 closest distance to " CA  MET A  40 " =    1.060
peak=    3.247 closest distance to " CA  MET A 105 " =    0.891
peak=    3.240 closest distance to " CB  ALA A 114 " =    1.406
peak=    3.239 closest distance to " O   HOH Z 217 " =    1.647
peak=    3.238 closest distance to " NE1 TRP A 274 " =    0.937
peak=    3.234 closest distance to " O   HOH Z  51 " =    1.659
peak=    3.233 closest distance to " O   ASN A  74 " =    1.511
peak=    3.233 closest distance to " O   HOH Z  64 " =    2.344
peak=    3.227 closest distance to " CG2 VAL A 197 " =    1.124
peak=    3.225 closest distance to " O   HOH Z 184 " =    1.944
peak=    3.225 closest distance to " O   HOH Z 126 " =    1.441
peak=    3.222 closest distance to " CB  ALA A   1 " =    4.628
peak=    3.222 closest distance to " CB  VAL A 265 " =    2.091
peak=    3.220 closest distance to " CA  SER A  32 " =    1.650
peak=    3.220 closest distance to " O   HOH Z  30 " =    1.710
peak=    3.218 closest distance to " CA  ALA A 291 " =    0.852
peak=    3.218 closest distance to " CA  ALA A  21 " =    1.196
peak=    3.217 closest distance to " O   HOH Z 145 " =    2.243
peak=    3.215 closest distance to " CB  ASN A 110 " =    1.132
peak=    3.209 closest distance to " O   HOH Z  66 " =    2.085
peak=    3.206 closest distance to " O   HOH Z 109 " =    2.527
peak=    3.203 closest distance to " CG1 VAL A 189 " =    1.887
peak=    3.201 closest distance to " O   HOH Z 407 " =    2.070
peak=    3.200 closest distance to " CG  LEU A 101 " =    1.147
peak=    3.199 closest distance to " CB  MET A  47 " =    1.069
peak=    3.198 closest distance to " O   MET A 105 " =    1.800
peak=    3.198 closest distance to " O   HOH Z 282 " =    1.424
peak=    3.197 closest distance to " NH2AARG A 190 " =    1.620
peak=    3.188 closest distance to " O   HOH Z  55 " =    2.005
peak=    3.185 closest distance to " CE AMET A  47 " =    1.339
peak=    3.175 closest distance to " O   HOH Z 130 " =    2.110
peak=    3.171 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.171 closest distance to " CG  MET A 113 " =    1.373
peak=    3.171 closest distance to " O   HOH Z 298 " =    2.549
peak=    3.171 closest distance to " O   HOH Z 374 " =    2.582
peak=    3.170 closest distance to " CB  GLU A 277 " =    1.021
peak=    3.166 closest distance to " CB  MET A  40 " =    0.828
peak=    3.164 closest distance to " O   HOH Z 282 " =    2.280
peak=    3.161 closest distance to " O   THR A 220 " =    1.464
peak=    3.158 closest distance to " OE1 GLN A 240 " =    1.616
peak=    3.157 closest distance to " O   HOH Z 288 " =    2.002
peak=    3.157 closest distance to " O   HOH Z 128 " =    2.004
peak=    3.154 closest distance to " O   HOH Z 359 " =    1.313
peak=    3.147 closest distance to " CB  GLU A 236 " =    1.350
peak=    3.136 closest distance to " CB  ALA A  10 " =    0.856
peak=    3.135 closest distance to " O   HOH Z 244 " =    1.675
peak=    3.135 closest distance to " O   HOH Z 386 " =    2.472
peak=    3.132 closest distance to " O   HOH Z 266 " =    3.376
peak=    3.131 closest distance to " ND1 HIS A  81 " =    1.645
peak=    3.130 closest distance to " O   HOH Z 414 " =    1.325
peak=    3.129 closest distance to " O   HOH Z 284 " =    1.394
peak=    3.114 closest distance to " NH1BARG A 145 " =    1.132
peak=    3.114 closest distance to " CB  ARG A 138 " =    0.882
peak=    3.109 closest distance to " O   HOH Z 284 " =    3.055
peak=    3.109 closest distance to " CG  GLN A  77 " =    2.437
peak=    3.107 closest distance to " CG  MET A  40 " =    2.338
peak=    3.104 closest distance to " CG1BVAL A  72 " =    1.415
peak=    3.103 closest distance to " CA  ALA A  51 " =    1.059
peak=    3.103 closest distance to " CB  ALA A 180 " =    1.356
peak=    3.098 closest distance to " O   HOH Z 151 " =    1.473
peak=    3.095 closest distance to " O   CYS A 168 " =    1.419
peak=    3.093 closest distance to " CB  ASP A 140 " =    0.850
peak=    3.093 closest distance to " O   HOH Z 409 " =    2.225
peak=    3.086 closest distance to " O   HOH Z 183 " =    1.365
peak=    3.084 closest distance to " CB  TYR A  30 " =    1.487
peak=    3.082 closest distance to " CB  ASP A 253 " =    0.831
peak=    3.077 closest distance to " O  BHOH Z 338 " =    2.350
peak=    3.066 closest distance to " OG  SER A  22 " =    2.900
peak=    3.051 closest distance to " O   HOH Z 273 " =    2.899
peak=    3.045 closest distance to " CG BARG A 102 " =    1.857
peak=    3.032 closest distance to " CD1BILE A 234 " =    1.009

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.726 - 5.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 212
   mapped sites are within: 0.726 - 5.457

peak=   -4.510 closest distance to " CB  PRO A 243 " =    2.527
peak=   -4.449 closest distance to " O   HOH Z 377 " =    1.878
peak=   -4.413 closest distance to " O   HOH Z  65 " =    0.977
peak=   -4.384 closest distance to " CD  ARG A 156 " =    1.991
peak=   -4.270 closest distance to " O   PRO A 198 " =    1.313
peak=   -4.202 closest distance to " O   HOH Z 407 " =    3.169
peak=   -4.201 closest distance to " O   HOH Z 266 " =    4.737
peak=   -4.148 closest distance to " CD1 LEU A 255 " =    2.990
peak=   -4.133 closest distance to " CA  GLY A  98 " =    1.813
peak=   -4.124 closest distance to " OG BSER A 134 " =    1.276
peak=   -4.095 closest distance to " CD  ARG A  14 " =    3.299
peak=   -4.028 closest distance to " O   HOH Z 185 " =    2.030
peak=   -4.023 closest distance to " O   HOH Z 351 " =    1.596
peak=   -4.003 closest distance to " O   SER A 135 " =    1.426
peak=   -3.958 closest distance to " O   HOH Z  52 " =    1.326
peak=   -3.931 closest distance to " O   HOH Z 389 " =    1.898
peak=   -3.907 closest distance to " O   HOH Z 316 " =    1.974
peak=   -3.904 closest distance to " O   HOH Z 231 " =    2.041
peak=   -3.852 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -3.852 closest distance to " CZ  PHE A  59 " =    1.493
peak=   -3.841 closest distance to " CB  ALA A  43 " =    2.428
peak=   -3.829 closest distance to " C   HIS A 108 " =    1.097
peak=   -3.821 closest distance to " ND2 ASN A  45 " =    1.113
peak=   -3.818 closest distance to " N   ALA A  43 " =    2.493
peak=   -3.802 closest distance to " CB  ASN A  39 " =    2.303
peak=   -3.799 closest distance to " O   HOH Z 198 " =    1.926
peak=   -3.783 closest distance to " CG  GLN A 223 " =    1.997
peak=   -3.765 closest distance to " CB  ALA A 248 " =    2.389
peak=   -3.762 closest distance to " CG1 VAL A 112 " =    3.025
peak=   -3.758 closest distance to " ND2 ASN A  45 " =    1.875
peak=   -3.757 closest distance to " N   THR A 157 " =    1.434
peak=   -3.750 closest distance to " CA  GLY A 203 " =    2.268
peak=   -3.743 closest distance to " O   PRO A 243 " =    2.330
peak=   -3.743 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.740 closest distance to " O   HOH Z 290 " =    1.221
peak=   -3.738 closest distance to " O   HOH Z  13 " =    1.720
peak=   -3.737 closest distance to " O   VAL A  67 " =    2.538
peak=   -3.714 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.707 closest distance to " O   HOH Z 372 " =    2.432
peak=   -3.685 closest distance to " O   HOH Z 152 " =    4.861
peak=   -3.677 closest distance to " O   VAL A 197 " =    1.734
peak=   -3.668 closest distance to " O   HOH Z 313 " =    1.735
peak=   -3.662 closest distance to " CB  ALA A 248 " =    1.967
peak=   -3.657 closest distance to " O   HOH Z 298 " =    2.402
peak=   -3.654 closest distance to " O   HOH Z  38 " =    1.591
peak=   -3.653 closest distance to " CG  PHE A 283 " =    2.580
peak=   -3.645 closest distance to " OD1 ASP A 191 " =    1.524
peak=   -3.641 closest distance to " CE2 TYR A  30 " =    2.681
peak=   -3.621 closest distance to " C   ALA A 158 " =    1.482
peak=   -3.616 closest distance to " O   ALA A 180 " =    1.191
peak=   -3.609 closest distance to " O   VAL A 189 " =    2.465
peak=   -3.600 closest distance to " C   ASN A 187 " =    1.840
peak=   -3.590 closest distance to " CB  PRO A  54 " =    2.397
peak=   -3.587 closest distance to " O   HOH Z 298 " =    1.105
peak=   -3.577 closest distance to " OD2 ASP A 191 " =    1.465
peak=   -3.575 closest distance to " O   HOH Z  43 " =    1.737
peak=   -3.571 closest distance to " CE  MET A 105 " =    2.386
peak=   -3.567 closest distance to " CB  ASP A  27 " =    2.398
peak=   -3.560 closest distance to " CB  CYS A 254 " =    2.085
peak=   -3.556 closest distance to " CG2 THR A  18 " =    2.797
peak=   -3.544 closest distance to " OD1 ASN A 187 " =    1.610
peak=   -3.532 closest distance to " ND2 ASN A 285 " =    2.073
peak=   -3.531 closest distance to " O   HOH Z 281 " =    2.862
peak=   -3.530 closest distance to " ND2 ASN A 249 " =    2.330
peak=   -3.520 closest distance to " C   LEU A 222 " =    0.726
peak=   -3.520 closest distance to " O   HOH Z  11 " =    1.929
peak=   -3.518 closest distance to " O   HOH Z  90 " =    2.657
peak=   -3.517 closest distance to " CD2 TYR A 293 " =    1.877
peak=   -3.512 closest distance to " O   HOH Z 131 " =    4.133
peak=   -3.508 closest distance to " O   HOH Z 352 " =    2.113
peak=   -3.504 closest distance to " N   GLN A  58 " =    1.697
peak=   -3.499 closest distance to " O   SER A  22 " =    2.552
peak=   -3.493 closest distance to " O   PHE A 218 " =    1.385
peak=   -3.492 closest distance to " O   HOH Z 140 " =    1.550
peak=   -3.484 closest distance to " O   HOH Z  60 " =    1.973
peak=   -3.479 closest distance to " O   HOH Z 384 " =    2.835
peak=   -3.477 closest distance to " CG1 VAL A 197 " =    2.205
peak=   -3.474 closest distance to " O   HOH Z 102 " =    1.576
peak=   -3.468 closest distance to " O   HOH Z 191 " =    5.397
peak=   -3.467 closest distance to " CE3 TRP A 123 " =    1.361
peak=   -3.462 closest distance to " CE1 PHE A  59 " =    2.040
peak=   -3.458 closest distance to " CA  GLY A 133 " =    1.940
peak=   -3.456 closest distance to " O   HOH Z 324 " =    2.038
peak=   -3.456 closest distance to " O   ASP A 162 " =    2.228
peak=   -3.450 closest distance to " CD  ARG A 139 " =    1.521
peak=   -3.449 closest distance to " NE  ARG A  36 " =    1.979
peak=   -3.448 closest distance to " O   ARG A 145 " =    1.422
peak=   -3.442 closest distance to " OG  SER A  87 " =    1.302
peak=   -3.439 closest distance to " O   HOH Z 166 " =    1.239
peak=   -3.436 closest distance to " OD1 ASN A 148 " =    1.631
peak=   -3.436 closest distance to " C   LEU A 143 " =    1.273
peak=   -3.429 closest distance to " CB  PHE A 192 " =    1.766
peak=   -3.425 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.419 closest distance to " CB  TYR A  15 " =    2.123
peak=   -3.418 closest distance to " CB  ALA A 291 " =    2.165
peak=   -3.415 closest distance to " CA  GLY A  57 " =    2.061
peak=   -3.414 closest distance to " CG  ASP A 231 " =    0.761
peak=   -3.413 closest distance to " CB  TRP A  85 " =    2.385
peak=   -3.413 closest distance to " O   SER A  95 " =    1.386
peak=   -3.411 closest distance to " CE  MET A  93 " =    1.113
peak=   -3.410 closest distance to " O   HOH Z 426 " =    2.328
peak=   -3.410 closest distance to " O   HOH Z 345 " =    2.219
peak=   -3.406 closest distance to " O   PRO A 163 " =    1.855
peak=   -3.397 closest distance to " NH2 ARG A  79 " =    1.992
peak=   -3.395 closest distance to " OG BSER A 134 " =    1.626
peak=   -3.391 closest distance to " CG2 VAL A 232 " =    2.002
peak=   -3.384 closest distance to " CG  ASN A  39 " =    1.698
peak=   -3.378 closest distance to " O   HOH Z 348 " =    1.784
peak=   -3.378 closest distance to " CA  GLY A  57 " =    2.192
peak=   -3.375 closest distance to " O   GLY A  17 " =    1.122
peak=   -3.373 closest distance to " CD1 LEU A 101 " =    2.286
peak=   -3.372 closest distance to " O   HOH Z 292 " =    1.479
peak=   -3.367 closest distance to " CD2 LEU A 237 " =    2.842
peak=   -3.366 closest distance to " CE  LYS A  76 " =    2.860
peak=   -3.355 closest distance to " CB  ALA A 131 " =    1.926
peak=   -3.350 closest distance to " CA  GLY A 241 " =    2.163
peak=   -3.342 closest distance to " CB  PRO A  90 " =    1.499
peak=   -3.328 closest distance to " O   HOH Z   1 " =    1.448
peak=   -3.328 closest distance to " O   HOH Z   9 " =    1.676
peak=   -3.324 closest distance to " NE2 GLN A 278 " =    1.826
peak=   -3.323 closest distance to " CZ2 TRP A 274 " =    0.947
peak=   -3.320 closest distance to " O   HOH Z 198 " =    1.764
peak=   -3.313 closest distance to " CE1 TYR A 169 " =    2.493
peak=   -3.309 closest distance to " O   HOH Z 111 " =    1.105
peak=   -3.304 closest distance to " CG  PRO A 163 " =    2.444
peak=   -3.303 closest distance to " CB  ALA A 100 " =    2.089
peak=   -3.302 closest distance to " CD  PRO A 198 " =    1.570
peak=   -3.302 closest distance to " O   HOH Z 350 " =    1.913
peak=   -3.301 closest distance to " O   HOH Z 111 " =    2.017
peak=   -3.301 closest distance to " OG  SER A  26 " =    1.245
peak=   -3.300 closest distance to " CD  LYS A 289 " =    2.394
peak=   -3.294 closest distance to " CG  GLN A  58 " =    1.307
peak=   -3.282 closest distance to " SD BMET A  47 " =    0.982
peak=   -3.282 closest distance to " O   HOH Z  28 " =    1.815
peak=   -3.281 closest distance to " O   HOH Z  60 " =    2.336
peak=   -3.279 closest distance to " OE1 GLN A  88 " =    1.183
peak=   -3.279 closest distance to " O   HOH Z 435 " =    2.960
peak=   -3.276 closest distance to " CD1 ILE A 239 " =    2.287
peak=   -3.276 closest distance to " O   HOH Z 134 " =    2.887
peak=   -3.273 closest distance to " OG  SER A 245 " =    1.260
peak=   -3.271 closest distance to " CZ  TYR A 169 " =    1.586
peak=   -3.271 closest distance to " O   HOH Z 410 " =    2.292
peak=   -3.270 closest distance to " O   HOH Z 418 " =    1.675
peak=   -3.264 closest distance to " OD2 ASP A 171 " =    1.941
peak=   -3.262 closest distance to " O   HOH Z 168 " =    1.808
peak=   -3.260 closest distance to " N   ASP A 171 " =    2.457
peak=   -3.258 closest distance to " O   VAL A  67 " =    2.821
peak=   -3.253 closest distance to " N   GLN A 122 " =    1.400
peak=   -3.251 closest distance to " NH1AARG A 275 " =    1.844
peak=   -3.251 closest distance to " CD  GLN A  88 " =    0.855
peak=   -3.249 closest distance to " O   HOH Z 114 " =    2.935
peak=   -3.246 closest distance to " CE  LYS A 166 " =    1.280
peak=   -3.244 closest distance to " O   HOH Z 427 " =    1.734
peak=   -3.240 closest distance to " OD2 ASP A 171 " =    1.749
peak=   -3.240 closest distance to " CG  LEU A 282 " =    2.445
peak=   -3.236 closest distance to " O   HOH Z 218 " =    3.505
peak=   -3.233 closest distance to " NH2AARG A 275 " =    5.457
peak=   -3.229 closest distance to " CE3 TRP A 274 " =    2.404
peak=   -3.228 closest distance to " NH2BARG A 275 " =    1.610
peak=   -3.220 closest distance to " O   HOH Z 432 " =    3.630
peak=   -3.219 closest distance to " C   ASN A 285 " =    2.335
peak=   -3.215 closest distance to " OD1 ASP A 171 " =    1.576
peak=   -3.214 closest distance to " O   ILE A  49 " =    1.732
peak=   -3.213 closest distance to " N   SER A 212 " =    1.934
peak=   -3.213 closest distance to " O   HOH Z 263 " =    3.130
peak=   -3.213 closest distance to " NE2 GLN A  58 " =    3.132
peak=   -3.206 closest distance to " O   HOH Z 318 " =    1.835
peak=   -3.205 closest distance to " O   TYR A  30 " =    2.844
peak=   -3.192 closest distance to " CD2 PHE A  61 " =    1.941
peak=   -3.192 closest distance to " N   ARG A 159 " =    1.917
peak=   -3.191 closest distance to " O   HOH Z 359 " =    3.272
peak=   -3.188 closest distance to " O   ALA A 180 " =    0.958
peak=   -3.186 closest distance to " SD  MET A 188 " =    2.399
peak=   -3.181 closest distance to " N   ARG A  14 " =    1.035
peak=   -3.181 closest distance to " OG  SER A  87 " =    1.637
peak=   -3.179 closest distance to " O   ALA A  10 " =    1.738
peak=   -3.177 closest distance to " OE2 GLU A 152 " =    1.019
peak=   -3.173 closest distance to " CE2 PHE A  61 " =    2.662
peak=   -3.170 closest distance to " OG  SER A  97 " =    2.076
peak=   -3.164 closest distance to " O   HOH Z 377 " =    1.325
peak=   -3.161 closest distance to " O   GLN A 240 " =    1.930
peak=   -3.160 closest distance to " OG  SER A 206 " =    1.835
peak=   -3.160 closest distance to " O   HOH Z 282 " =    4.556
peak=   -3.153 closest distance to " OD1 ASP A 200 " =    1.385
peak=   -3.150 closest distance to " O   HOH Z 211 " =    1.466
peak=   -3.149 closest distance to " O   HOH Z 114 " =    0.758
peak=   -3.148 closest distance to " O   GLY A  80 " =    2.359
peak=   -3.148 closest distance to " CA  ALA A  34 " =    2.422
peak=   -3.148 closest distance to " O   HOH Z 326 " =    1.562
peak=   -3.147 closest distance to " O   ALA A 161 " =    1.598
peak=   -3.147 closest distance to " O   HOH Z 300 " =    1.998
peak=   -3.140 closest distance to " O   PRO A 243 " =    2.035
peak=   -3.130 closest distance to " O   HOH Z  98 " =    2.350
peak=   -3.128 closest distance to " ND2BASN A 224 " =    1.640
peak=   -3.120 closest distance to " CG2 THR A 178 " =    2.152
peak=   -3.119 closest distance to " O   HOH Z  37 " =    1.760
peak=   -3.107 closest distance to " N   ASP A 270 " =    1.377
peak=   -3.105 closest distance to " OE1 GLN A 183 " =    1.508
peak=   -3.104 closest distance to " O   HOH Z 250 " =    1.403
peak=   -3.093 closest distance to " N   SER A 276 " =    1.181
peak=   -3.091 closest distance to " O   SER A  62 " =    2.102
peak=   -3.083 closest distance to " O   HOH Z 346 " =    1.651
peak=   -3.072 closest distance to " O   HOH Z  97 " =    1.731
peak=   -3.072 closest distance to " OE1 GLN A  58 " =    3.003
peak=   -3.071 closest distance to " O   HOH Z 263 " =    5.209
peak=   -3.069 closest distance to " NH2 ARG A 219 " =    1.759
peak=   -3.065 closest distance to " O   HOH Z 438 " =    1.126
peak=   -3.060 closest distance to " CD2 LEU A 237 " =    2.344
peak=   -3.056 closest distance to " O   HOH Z  73 " =    2.237
peak=   -3.045 closest distance to " CG1AVAL A  41 " =    2.884
peak=   -3.027 closest distance to " C   ALA A 114 " =    2.304
peak=   -3.012 closest distance to " CD2 TYR A 293 " =    2.144

================= 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    :  0.4082 0.4069   6.217336e+00   6.212882e+00
   1_bss:  0.3962 0.3986   6.203662e+00   6.197279e+00
   1_xyz:  0.2672 0.3044   5.889866e+00   5.972244e+00
   1_adp:  0.2443 0.3179   5.843662e+00   6.004048e+00
   1_occ:  0.2440 0.3175   5.842693e+00   6.003395e+00
   2_bss:  0.2420 0.3123   5.833165e+00   5.992676e+00
   2_xyz:  0.1902 0.2432   5.609673e+00   5.793449e+00
   2_adp:  0.1803 0.2309   5.564521e+00   5.751914e+00
   2_occ:  0.1801 0.2310   5.564151e+00   5.752221e+00
   3_bss:  0.1798 0.2297   5.559923e+00   5.746704e+00
   3_xyz:  0.1437 0.1902   5.356997e+00   5.571028e+00
   3_adp:  0.1323 0.1817   5.289489e+00   5.516596e+00
   3_occ:  0.1322 0.1817   5.289469e+00   5.516625e+00
   4_bss:  0.1325 0.1817   5.288634e+00   5.514913e+00
   4_xyz:  0.1188 0.1681   5.197559e+00   5.439789e+00
   4_adp:  0.1167 0.1615   5.172100e+00   5.407064e+00
   4_occ:  0.1166 0.1616   5.172085e+00   5.407100e+00
   5_bss:  0.1166 0.1615   5.171773e+00   5.406742e+00
   5_xyz:  0.1128 0.1568   5.145345e+00   5.384485e+00
   5_adp:  0.1115 0.1577   5.144545e+00   5.390993e+00
   5_occ:  0.1115 0.1578   5.144579e+00   5.391142e+00
   5_bss:  0.1114 0.1577   5.144589e+00   5.391131e+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:  0.357  50.000  -1.735   3.202  -1.743   0.000  -0.000  -0.000
   1_xyz:  0.357  50.000  -1.735   3.202  -1.743   0.000  -0.000  -0.000
   1_adp:  0.357  50.000  -1.735   3.202  -1.743   0.000  -0.000  -0.000
   1_occ:  0.357  50.000  -1.735   3.202  -1.743   0.000  -0.000  -0.000
   2_bss:  0.342  57.920  -1.781  -0.366  -1.316  -0.000  -0.000  -0.000
   2_xyz:  0.342  57.920  -1.781  -0.366  -1.316  -0.000  -0.000  -0.000
   2_adp:  0.342  57.920  -1.781  -0.366  -1.316  -0.000  -0.000  -0.000
   2_occ:  0.342  57.920  -1.781  -0.366  -1.316  -0.000  -0.000  -0.000
   3_bss:  0.330  50.244  -1.994  -1.676  -1.195  -0.000  -0.000  -0.000
   3_xyz:  0.330  50.244  -1.994  -1.676  -1.195  -0.000  -0.000  -0.000
   3_adp:  0.330  50.244  -1.994  -1.676  -1.195  -0.000  -0.000  -0.000
   3_occ:  0.330  50.244  -1.994  -1.676  -1.195  -0.000  -0.000  -0.000
   4_bss:  0.324  53.288  -2.249  -2.489  -1.472  -0.000  -0.000  -0.000
   4_xyz:  0.324  53.288  -2.249  -2.489  -1.472  -0.000  -0.000  -0.000
   4_adp:  0.324  53.288  -2.249  -2.489  -1.472  -0.000  -0.000  -0.000
   4_occ:  0.324  53.288  -2.249  -2.489  -1.472  -0.000  -0.000  -0.000
   5_bss:  0.324  53.288  -2.274  -2.646  -1.432  -0.000  -0.000  -0.000
   5_xyz:  0.324  53.288  -2.274  -2.646  -1.432  -0.000  -0.000  -0.000
   5_adp:  0.324  53.288  -2.274  -2.646  -1.432  -0.000  -0.000  -0.000
   5_occ:  0.324  53.288  -2.274  -2.646  -1.432  -0.000  -0.000  -0.000
   5_bss:  0.324  53.290  -2.133  -2.575  -1.294  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.940 0.5603  0.7495    53514.178
   1_bss:  46.244 0.5673  0.7578    50832.339
   1_xyz:  30.945 0.7489  0.9431    24857.376
   1_adp:  32.790 0.7269  0.9202    26985.504
   1_occ:  32.799 0.7267  0.9195    26929.748
   2_bss:  32.020 0.7354  0.8978    25877.670
   2_xyz:  24.186 0.8195  0.9695    15215.334
   2_adp:  22.547 0.8370  0.9850    13795.689
   2_occ:  22.560 0.8368  0.9845    13809.394
   3_bss:  22.362 0.8385  0.9692    13539.654
   3_xyz:  18.141 0.8787  0.9947     9241.807
   3_adp:  16.856 0.8908  0.9932     8358.034
   3_occ:  16.857 0.8908  0.9931     8356.161
   4_bss:  16.805 0.8912  0.9777     8313.345
   4_xyz:  15.136 0.9055  0.9843     7051.309
   4_adp:  14.372 0.9120  0.9827     6632.113
   4_occ:  14.375 0.9120  0.9826     6627.710
   5_bss:  14.367 0.9120  0.9811     6623.846
   5_xyz:  13.900 0.9158  0.9826     6301.345
   5_adp:  13.976 0.9154  0.9769     6342.437
   5_occ:  13.978 0.9154  0.9769     6344.977
   5_bss:  13.979 0.9154  0.9811     6345.934
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7159e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7159e-01
   1_xyz:   1.501  0.012  0.101 15.662  0.007  4.108   1.1830e-01
   1_adp:   1.501  0.012  0.101 15.662  0.007  4.108   1.1830e-01
   1_occ:   1.501  0.012  0.101 15.662  0.007  4.108   1.1830e-01
   2_bss:   1.501  0.012  0.101 15.662  0.007  4.108   1.1830e-01
   2_xyz:   0.982  0.006  0.068 14.269  0.004  4.117   5.6178e-02
   2_adp:   0.982  0.006  0.068 14.269  0.004  4.117   5.6178e-02
   2_occ:   0.982  0.006  0.068 14.269  0.004  4.117   5.6178e-02
   3_bss:   0.982  0.006  0.068 14.269  0.004  4.117   5.6178e-02
   3_xyz:   0.922  0.005  0.067 14.394  0.004  4.111   5.1598e-02
   3_adp:   0.922  0.005  0.067 14.394  0.004  4.111   5.1598e-02
   3_occ:   0.922  0.005  0.067 14.394  0.004  4.111   5.1598e-02
   4_bss:   0.922  0.005  0.067 14.394  0.004  4.111   5.1598e-02
   4_xyz:   0.951  0.006  0.072 14.499  0.004  4.115   5.4741e-02
   4_adp:   0.951  0.006  0.072 14.499  0.004  4.115   5.4741e-02
   4_occ:   0.951  0.006  0.072 14.499  0.004  4.115   5.4741e-02
   5_bss:   0.951  0.006  0.072 14.499  0.004  4.115   5.4741e-02
   5_xyz:   0.932  0.006  0.070 14.485  0.004  4.110   5.4021e-02
   5_adp:   0.932  0.006  0.070 14.485  0.004  4.110   5.4021e-02
   5_occ:   0.932  0.006  0.070 14.485  0.004  4.110   5.4021e-02
   5_bss:   0.932  0.006  0.070 14.485  0.004  4.110   5.4021e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3998e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3998e-01
   1_xyz:   9.177  0.092  0.458 88.184  0.045  2.072   1.0321e-01
   1_adp:   9.177  0.092  0.458 88.184  0.045  2.072   1.0321e-01
   1_occ:   9.177  0.092  0.458 88.184  0.045  2.072   1.0321e-01
   2_bss:   9.177  0.092  0.458 88.184  0.045  2.072   1.0321e-01
   2_xyz:   7.039  0.038  0.218 84.351  0.031  2.354   5.4934e-02
   2_adp:   7.039  0.038  0.218 84.351  0.031  2.354   5.4934e-02
   2_occ:   7.039  0.038  0.218 84.351  0.031  2.354   5.4934e-02
   3_bss:   7.039  0.038  0.218 84.351  0.031  2.354   5.4934e-02
   3_xyz:   7.133  0.037  0.220 84.151  0.031  2.326   4.6112e-02
   3_adp:   7.133  0.037  0.220 84.151  0.031  2.326   4.6112e-02
   3_occ:   7.133  0.037  0.220 84.151  0.031  2.326   4.6112e-02
   4_bss:   7.133  0.037  0.220 84.151  0.031  2.326   4.6112e-02
   4_xyz:   7.620  0.038  0.214 84.646  0.037  2.342   4.9622e-02
   4_adp:   7.620  0.038  0.214 84.646  0.037  2.342   4.9622e-02
   4_occ:   7.620  0.038  0.214 84.646  0.037  2.342   4.9622e-02
   5_bss:   7.620  0.038  0.214 84.646  0.037  2.342   4.9622e-02
   5_xyz:   7.769  0.039  0.216 84.487  0.035  2.313   5.0978e-02
   5_adp:   7.769  0.039  0.216 84.487  0.035  2.313   5.0978e-02
   5_occ:   7.769  0.039  0.216 84.487  0.035  2.313   5.0978e-02
   5_bss:   7.769  0.039  0.216 84.487  0.035  2.313   5.0978e-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:  97.78   0.00  17.91  71.92   0.00  13.73  97.78   4.28  40.64
   1_occ:  97.78   0.00  17.91  71.92   0.00  13.73  97.78   4.28  40.64
   2_bss:  97.78   0.00  17.91  71.92   0.00  13.73  97.78   4.28  40.64
   2_xyz:  97.78   0.00  17.91  71.92   0.00  13.73  97.78   4.28  40.64
   2_adp:  96.94   0.00  17.78  72.47   0.00  13.63  96.94   5.82  40.39
   2_occ:  96.94   0.00  17.78  72.47   0.00  13.63  96.94   5.82  40.39
   3_bss:  96.94   0.00  17.78  72.47   0.00  13.63  96.94   5.82  40.39
   3_xyz:  96.94   0.00  17.78  72.47   0.00  13.63  96.94   5.82  40.39
   3_adp: 100.54   0.00  18.07  89.86   0.00  13.32 100.54   6.72  43.97
   3_occ: 100.54   0.00  18.07  89.86   0.00  13.32 100.54   6.72  43.97
   4_bss: 100.54   0.00  18.07  89.86   0.00  13.32 100.54   6.72  43.97
   4_xyz: 100.54   0.00  18.07  89.86   0.00  13.32 100.54   6.72  43.97
   4_adp:  96.49   0.46  17.43  90.94   0.46  13.00  96.49   6.49  41.60
   4_occ:  96.49   0.46  17.43  90.94   0.46  13.00  96.49   6.49  41.60
   5_bss:  96.49   0.46  17.43  90.94   0.46  13.00  96.49   6.49  41.60
   5_xyz:  96.49   0.46  17.43  90.94   0.46  13.00  96.49   6.49  41.60
   5_adp: 101.08   0.00  17.54 101.08   0.00  12.98  98.09   5.93  42.39
   5_occ: 101.08   0.00  17.54 101.08   0.00  12.98  98.09   5.93  42.39
   5_bss: 101.08   0.00  17.54 101.08   0.00  12.98  98.10   5.94  42.40
------------------------------------------------------------------------
 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:    1.426    0.036    0.426
   1_adp:    1.426    0.036    0.426
   1_occ:    1.426    0.036    0.426
   2_bss:    1.426    0.036    0.426
   2_xyz:    1.284    0.033    0.493
   2_adp:    1.284    0.033    0.493
   2_occ:    1.284    0.033    0.493
   3_bss:    1.284    0.033    0.493
   3_xyz:    1.233    0.067    0.594
   3_adp:    1.233    0.067    0.594
   3_occ:    1.233    0.067    0.594
   4_bss:    1.233    0.067    0.594
   4_xyz:    1.272    0.052    0.625
   4_adp:    1.272    0.052    0.625
   4_occ:    1.272    0.052    0.625
   5_bss:    1.272    0.052    0.625
   5_xyz:    1.400    0.034    0.641
   5_adp:    1.400    0.034    0.641
   5_occ:    1.400    0.034    0.641
   5_bss:    1.400    0.034    0.641
------------------------------------------------------------------------

CPU time actual refinement: 357.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/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_862/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_862/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.74 
  Macro-tasks:
    bulk solvent and scale       = 35.73  
    individual site refinement   = 153.09 
    weights calculation          = 30.70  
    collect and process          = 6.66   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.28 
  Micro-tasks:
    mask                            = 1.91   
    f_calc                          = 120.54 
    alpha_beta                      = 8.56   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 128.60 
    fmodel                         = 6.62   
    r_factors                      = 0.18   
    phase_errors                   = 10.49  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 278.39 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.035 micro seconds
Total CPU time: 6.19 minutes
from_scatterers_fft:    653 calls, 120.14 s
gradients_fft:          598 calls, 114.79 s

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

# Date 2008-01-16 Time 05:51:09 PST -0800 (1200491469.19 s)
Start R-work = 0.4082, R-free = 0.4069 (no bulk solvent and anisotropic scale)
Final R-work = 0.1354, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.3962, R-free = 0.3986
Final R-work = 0.1114, R-free = 0.1577