# Date 2008-01-16 Time 05:09:29 PST -0800 (1200488969.90 s)
#phil __OFF__

Command line arguments: "../618.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8797
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 618

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== 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: (70.25, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.96157
Completeness in resolution range: 0.96431
Completeness with d_max=infinity: 0.961376

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9616

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: (70.25, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.96157
Completeness in resolution range: 0.96431
Completeness with d_max=infinity: 0.961376

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.1977 [2126/2151]  1916   210   9.9%
  bin  2:  4.1977 -  3.3442 [2050/2070]  1844   206  10.0%
  bin  3:  3.3442 -  2.9250 [2032/2051]  1826   206  10.1%
  bin  4:  2.9250 -  2.6592 [2004/2034]  1809   195   9.7%
  bin  5:  2.6592 -  2.4696 [2000/2019]  1801   199   9.9%
  bin  6:  2.4696 -  2.3245 [1989/2014]  1783   206  10.4%
  bin  7:  2.3245 -  2.2085 [1946/1974]  1752   194  10.0%
  bin  8:  2.2085 -  2.1126 [1987/2023]  1787   200  10.1%
  bin  9:  2.1126 -  2.0315 [1953/1995]  1760   193   9.9%
  bin 10:  2.0315 -  1.9616 [1502/1983]  1352   150  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.77 -     2.39: 40
        2.39 -     3.02: 2099
        3.02 -     3.65: 4748
        3.65 -     4.27: 9244
        4.27 -     4.90: 12666
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.767 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.877 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.880 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
  ... (remaining 28792 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_618/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/model_refine_001.geo

CPU time processing inputs: 9.61


============================ 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 = 70.25 45.9914 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4315   r_free= 0.4295   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.242234                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6821 0.99   1390  155 0.3520 0.3509      6.5143      6.5177|
|  2:  4.6821 -  3.7355 0.99   1334  147 0.3657 0.3518      6.7418      6.6725|
|  3:  3.7355 -  3.2689 0.99   1302  142 0.3945 0.3887      6.6305      6.7201|
|  4:  3.2689 -  2.9726 0.99   1305  153 0.4065 0.4273      6.4854      6.4536|
|  5:  2.9726 -  2.7610 0.99   1293  142 0.4551 0.4313      6.3334      6.3253|
|  6:  2.7610 -  2.5991 0.99   1283  138 0.4591 0.4819      6.2496      6.2235|
|  7:  2.5991 -  2.4696 0.99   1289  139 0.4615 0.4527      6.2094      6.1968|
|  8:  2.4696 -  2.3625 0.98   1261  148 0.4771 0.4464      6.1558      6.1343|
|  9:  2.3625 -  2.2719 0.98   1266  142 0.4767 0.4672      6.1056      6.1003|
| 10:  2.2719 -  2.1937 1.00   1283  138 0.4691 0.5034      6.0633      6.1171|
| 11:  2.1937 -  2.1253 0.97   1255  140 0.4826 0.4929      6.0165      6.0623|
| 12:  2.1253 -  2.0647 0.98   1250  139 0.4820 0.4778      5.9589       5.991|
| 13:  2.0647 -  2.0105 0.99   1290  143 0.4762 0.4799      5.8556      5.7945|
| 14:  2.0105 -  1.9616 0.66    829   93 0.5194 0.4407      5.8746      5.7681|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.6821  1390   155  0.72  32.31   0.84     0.77      64650.31|
|  2:  4.6821 -  3.7355  1334   147  0.74  31.79   0.93     0.86      91010.40|
|  3:  3.7355 -  3.2689  1302   142  0.66  39.25   0.96     0.85      97073.41|
|  4:  3.2689 -  2.9726  1305   153  0.58  45.76   0.96     0.77      89500.23|
|  5:  2.9726 -  2.7610  1293   142  0.49  52.28   0.91     0.69      71834.82|
|  6:  2.7610 -  2.5991  1283   138  0.47  54.40   0.92     0.65      64122.70|
|  7:  2.5991 -  2.4696  1289   139  0.45  55.67   0.94     0.63      57748.73|
|  8:  2.4696 -  2.3625  1261   148  0.44  56.79   0.95     0.64      52956.40|
|  9:  2.3625 -  2.2719  1266   142  0.46  55.64   0.94     0.64      46621.87|
| 10:  2.2719 -  2.1937  1283   138  0.45  55.70   0.98     0.66      42393.74|
| 11:  2.1937 -  2.1253  1255   140  0.43  57.41   0.99     0.65      41151.44|
| 12:  2.1253 -  2.0647  1250   139  0.44  57.17   1.01     0.68      37331.60|
| 13:  2.0647 -  2.0105  1290   143  0.45  56.54   0.99     0.70      30597.34|
| 14:  2.0105 -  1.9616   829    93  0.53  50.07   0.97     0.74      21604.71|
|alpha:            min =        0.63 max =            0.86 mean =         0.71|
|beta:             min =    21604.71 max =        97073.41 mean =     58986.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.85|
|phase err.(test): min =        0.00 max =           89.97 mean =        50.21|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.833779             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.306   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.835287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.476   (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 |  1.767 -  2.080:       13 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.080 -  2.393:       27 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.393 -  2.707:      156 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.707 -  3.020:     1943 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.020 -  3.333:     1927 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.333 -  3.647:     2821 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.647 -  3.960:     4765 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.960 -  4.273:     4479 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.273 -  4.587:     5751 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.587 -  4.900:     6915 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.767 |       0.390 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4315   r_free= 0.4295   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.242234                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4188   r_free= 0.4169   ksol= 0.34   Bsol= 26.50   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,2.81,0.37,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.232814                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.864191              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.256   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.958973              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.362   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4188      final r-factor (work) = 0.2896          |
| start r-factor (free) = 0.4169      final r-factor (free) = 0.3215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7841 = 8.86 * 0.50 * 6.2295 + 1.00 * 0.1745                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.9784 = 8.86 * 0.50 * 6.0589 + 1.00 * 0.1246                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2896      final r-factor (work) = 0.2627          |
| start r-factor (free) = 0.3215      final r-factor (free) = 0.3388          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8164 = 0.96 * 1.00 * 6.0589 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6616 = 0.96 * 1.00 * 5.8872 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.68   18.09    None  None   None       |
|    all(noH): 2823   0      0.00    95.68   18.09    None  None   None       |
|    Sol.    : 438    0      2.34    95.68   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    78.56   14.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.568:  900   |   5:    47.838 -  57.406:   99        |
|      1:     9.568 -  19.135:  993   |   6:    57.406 -  66.974:   52        |
|      2:    19.135 -  28.703:  416   |   7:    66.974 -  76.541:   14        |
|      3:    28.703 -  38.271:  197   |   8:    76.541 -  86.109:    6        |
|      4:    38.271 -  47.838:  145   |   9:    86.109 -  95.677:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2627 r_free = 0.3388             target_work(ml) = 5.903         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2624 r_free = 0.3391             target_work(ml) = 5.902         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2624   r_free= 0.3391   ksol= 0.34   Bsol= 26.50   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,2.81,0.37,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.902169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3357   ksol= 0.33   Bsol= 38.95   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.26,-0.56,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.894916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.907826              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.160   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2604      final r-factor (work) = 0.1912          |
| start r-factor (free) = 0.3357      final r-factor (free) = 0.2451          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5090 = 5.91 * 0.50 * 5.8852 + 1.00 * 0.1246                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1428 = 5.91 * 0.50 * 5.7796 + 1.00 * 0.0705                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1713          |
| start r-factor (free) = 0.2451      final r-factor (free) = 0.2219          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3834 = 0.24 * 1.00 * 5.7796 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3238 = 0.24 * 1.00 * 5.5594 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.65   17.11    None  None   None       |
|    all(noH): 2823   0      0.00    88.65   17.11    None  None   None       |
|    Sol.    : 438    0      5.45    88.65   39.20    None  None   None       |
|    Mac.    : 2385   0      0.00    79.85   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.865:  750   |   5:    44.324 -  53.189:  119        |
|      1:     8.865 -  17.730: 1255   |   6:    53.189 -  62.053:   60        |
|      2:    17.730 -  26.594:  324   |   7:    62.053 -  70.918:   19        |
|      3:    26.594 -  35.459:  157   |   8:    70.918 -  79.783:    3        |
|      4:    35.459 -  44.324:  134   |   9:    79.783 -  88.648:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1713 r_free = 0.2219             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1710 r_free = 0.2216             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1710   r_free= 0.2216   ksol= 0.33   Bsol= 38.95   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.26,-0.56,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.510363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1707   r_free= 0.2204   ksol= 0.32   Bsol= 38.95   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.43,-0.87,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.505421                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.476912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.906  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.566  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1707      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2204      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7332 = 3.48 * 0.50 * 5.5582 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4389 = 3.48 * 0.50 * 5.3954 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6586 = 0.31 * 1.00 * 5.3954 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6142 = 0.31 * 1.00 * 5.2497 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    85.73   17.02    None  None   None       |
|    all(noH): 2823   0      0.82    85.73   17.02    None  None   None       |
|    Sol.    : 438    0      5.78    85.73   40.56    None  None   None       |
|    Mac.    : 2385   0      0.82    84.54   12.70    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:     0.822 -   9.313:  902   |   5:    43.276 -  51.766:  104        |
|      1:     9.313 -  17.803: 1178   |   6:    51.766 -  60.257:   88        |
|      2:    17.803 -  26.294:  257   |   7:    60.257 -  68.748:   41        |
|      3:    26.294 -  34.785:  137   |   8:    68.748 -  77.239:    9        |
|      4:    34.785 -  43.276:  104   |   9:    77.239 -  85.730:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1720             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1245 r_free = 0.1718             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1718   ksol= 0.32   Bsol= 38.95   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.43,-0.87,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.225567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1715   ksol= 0.32   Bsol= 40.20   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.21,-1.31,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225615                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.408858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.347  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.353329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.905  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0137 = 3.41 * 0.50 * 5.2536 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9008 = 3.41 * 0.50 * 5.1830 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8396 = 0.35 * 1.00 * 5.1830 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8235 = 0.35 * 1.00 * 5.1373 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    89.65   16.84    None  None   None       |
|    all(noH): 2823   0      0.54    89.65   16.84    None  None   None       |
|    Sol.    : 438    0      6.32    85.65   39.98    None  None   None       |
|    Mac.    : 2385   0      0.54    89.65   12.59    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:     0.537 -   9.448:  945   |   5:    45.094 -  54.006:  101        |
|      1:     9.448 -  18.360: 1181   |   6:    54.006 -  62.917:   62        |
|      2:    18.360 -  27.271:  241   |   7:    62.917 -  71.829:   35        |
|      3:    27.271 -  36.183:  134   |   8:    71.829 -  80.740:    4        |
|      4:    36.183 -  45.094:  116   |   9:    80.740 -  89.652:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1101 r_free = 0.1573             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1572             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1572   ksol= 0.32   Bsol= 40.20   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.21,-1.31,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.130504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1571   ksol= 0.32   Bsol= 40.95   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.29,-1.31,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.130269                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.067132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.641  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211795              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.881  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3761 = 2.07 * 0.50 * 5.1371 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3570 = 2.07 * 0.50 * 5.1307 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0950 = 0.21 * 1.00 * 5.1307 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0932 = 0.21 * 1.00 * 5.1253 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    90.10   16.52    None  None   None       |
|    all(noH): 2823   0      0.91    90.10   16.52    None  None   None       |
|    Sol.    : 438    0      6.27    82.82   38.58    None  None   None       |
|    Mac.    : 2385   0      0.91    90.10   12.47    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:     0.912 -   9.831: 1059   |   5:    45.508 -  54.428:   89        |
|      1:     9.831 -  18.750: 1100   |   6:    54.428 -  63.347:   51        |
|      2:    18.750 -  27.670:  221   |   7:    63.347 -  72.266:   24        |
|      3:    27.670 -  36.589:  140   |   8:    72.266 -  81.185:    4        |
|      4:    36.589 -  45.508:  131   |   9:    81.185 -  90.105:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1100 r_free = 0.1550             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1550             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1550   ksol= 0.32   Bsol= 40.95   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.29,-1.31,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122571                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6821 0.99   1390  155 0.0975 0.1212      5.3565      5.5101|
|  2:  4.6821 -  3.7355 0.99   1334  147 0.0855 0.1183      5.4448      5.6487|
|  3:  3.7355 -  3.2689 0.99   1302  142 0.1068 0.1514      5.4805      5.8613|
|  4:  3.2689 -  2.9726 0.99   1305  153 0.1210 0.1506      5.4471       5.568|
|  5:  2.9726 -  2.7610 0.99   1293  142 0.1302 0.1828      5.3078      5.5445|
|  6:  2.7610 -  2.5991 0.99   1283  138 0.1174 0.1627      5.1874      5.3905|
|  7:  2.5991 -  2.4696 0.99   1289  139 0.1244 0.1534      5.1434      5.3538|
|  8:  2.4696 -  2.3625 0.98   1261  148 0.1132 0.1707      5.0245      5.3173|
|  9:  2.3625 -  2.2719 0.98   1266  142 0.1101 0.1682      4.9896      5.2346|
| 10:  2.2719 -  2.1937 1.00   1283  138 0.1106 0.1805      4.9343       5.244|
| 11:  2.1937 -  2.1253 0.97   1255  140 0.1127 0.1721      4.9392      5.2597|
| 12:  2.1253 -  2.0647 0.98   1250  139 0.1091 0.1629      4.8555      5.1227|
| 13:  2.0647 -  2.0105 0.99   1290  143 0.1087 0.1773      4.7495      5.0636|
| 14:  2.0105 -  1.9616 0.66    829   93 0.0990 0.1435      4.6216      4.8227|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.6821  1390   155  0.94   8.63   0.99     0.96       6607.24|
|  2:  4.6821 -  3.7355  1334   147  0.95   7.95   1.03     1.02       9104.43|
|  3:  3.7355 -  3.2689  1302   142  0.93  11.30   1.03     1.03      10393.38|
|  4:  3.2689 -  2.9726  1305   153  0.92  13.52   1.01     0.99      10094.34|
|  5:  2.9726 -  2.7610  1293   142  0.90  15.39   1.00     0.97       7778.35|
|  6:  2.7610 -  2.5991  1283   138  0.90  15.56   0.99     0.97       6795.23|
|  7:  2.5991 -  2.4696  1289   139  0.91  15.01   1.00     0.97       5816.22|
|  8:  2.4696 -  2.3625  1261   148  0.91  14.53   0.99     0.97       4783.34|
|  9:  2.3625 -  2.2719  1266   142  0.92  14.29   1.01     0.99       4571.64|
| 10:  2.2719 -  2.1937  1283   138  0.91  14.98   1.01     0.98       4149.34|
| 11:  2.1937 -  2.1253  1255   140  0.90  15.87   1.00     0.96       4228.67|
| 12:  2.1253 -  2.0647  1250   139  0.92  14.70   1.02     1.01       3780.83|
| 13:  2.0647 -  2.0105  1290   143  0.91  15.34   1.01     1.00       3077.99|
| 14:  2.0105 -  1.9616   829    93  0.93  13.32   0.99     0.97       2315.51|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2315.51 max =        10393.38 mean =      6090.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.55|
|phase err.(test): min =        0.00 max =           88.95 mean =        13.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1550   ksol= 0.32   Bsol= 40.91   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.23,-1.19,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1550   ksol= 0.32   Bsol= 40.91   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.23,-1.19,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122625                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6821 0.99   1390  155 0.0975 0.1213      5.3578      5.5116|
|  2:  4.6821 -  3.7355 0.99   1334  147 0.0855 0.1183      5.4451      5.6483|
|  3:  3.7355 -  3.2689 0.99   1302  142 0.1068 0.1514      5.4804      5.8614|
|  4:  3.2689 -  2.9726 0.99   1305  153 0.1210 0.1506      5.4471      5.5681|
|  5:  2.9726 -  2.7610 0.99   1293  142 0.1302 0.1827      5.3076      5.5441|
|  6:  2.7610 -  2.5991 0.99   1283  138 0.1174 0.1627      5.1872      5.3902|
|  7:  2.5991 -  2.4696 0.99   1289  139 0.1244 0.1534      5.1435      5.3542|
|  8:  2.4696 -  2.3625 0.98   1261  148 0.1132 0.1706      5.0246       5.317|
|  9:  2.3625 -  2.2719 0.98   1266  142 0.1101 0.1682      4.9895      5.2345|
| 10:  2.2719 -  2.1937 1.00   1283  138 0.1106 0.1807      4.9344      5.2449|
| 11:  2.1937 -  2.1253 0.97   1255  140 0.1127 0.1720      4.9394      5.2599|
| 12:  2.1253 -  2.0647 0.98   1250  139 0.1090 0.1630      4.8554      5.1229|
| 13:  2.0647 -  2.0105 0.99   1290  143 0.1087 0.1772      4.7492       5.063|
| 14:  2.0105 -  1.9616 0.66    829   93 0.0989 0.1431      4.6208      4.8213|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.6821  1390   155  0.94   8.65   0.99     0.96       6632.19|
|  2:  4.6821 -  3.7355  1334   147  0.95   7.97   1.03     1.02       9118.92|
|  3:  3.7355 -  3.2689  1302   142  0.93  11.30   1.03     1.03      10393.42|
|  4:  3.2689 -  2.9726  1305   153  0.92  13.52   1.01     0.99      10091.01|
|  5:  2.9726 -  2.7610  1293   142  0.90  15.38   1.00     0.97       7773.76|
|  6:  2.7610 -  2.5991  1283   138  0.90  15.55   0.99     0.97       6793.31|
|  7:  2.5991 -  2.4696  1289   139  0.91  15.01   1.00     0.97       5815.95|
|  8:  2.4696 -  2.3625  1261   148  0.91  14.53   1.00     0.98       4782.76|
|  9:  2.3625 -  2.2719  1266   142  0.92  14.29   1.01     0.99       4572.10|
| 10:  2.2719 -  2.1937  1283   138  0.91  14.99   1.01     0.98       4152.49|
| 11:  2.1937 -  2.1253  1255   140  0.90  15.87   1.01     0.96       4231.89|
| 12:  2.1253 -  2.0647  1250   139  0.92  14.70   1.03     1.02       3781.23|
| 13:  2.0647 -  2.0105  1290   143  0.91  15.33   1.02     1.01       3074.67|
| 14:  2.0105 -  1.9616   829    93  0.93  13.29   1.00     0.97       2310.12|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2310.12 max =        10393.42 mean =      6092.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.55|
|phase err.(test): min =        0.00 max =           88.96 mean =        13.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    90.07   16.49    None  None   None       |
|    all(noH): 2823   0      0.88    90.07   16.49    None  None   None       |
|    Sol.    : 438    0      6.24    82.79   38.55    None  None   None       |
|    Mac.    : 2385   0      0.88    90.07   12.44    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:     0.880 -   9.800: 1059   |   5:    45.477 -  54.396:   89        |
|      1:     9.800 -  18.719: 1100   |   6:    54.396 -  63.316:   51        |
|      2:    18.719 -  27.638:  221   |   7:    63.316 -  72.235:   24        |
|      3:    27.638 -  36.558:  140   |   8:    72.235 -  81.154:    4        |
|      4:    36.558 -  45.477:  131   |   9:    81.154 -  90.074:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 4.558
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 305
   mapped sites are within: 0.707 - 4.558

peak=    6.532 closest distance to " NE2 GLN A  11 " =    1.301
peak=    5.733 closest distance to " O   HOH Z 126 " =    2.005
peak=    5.655 closest distance to " NH2 ARG A  56 " =    2.074
peak=    5.512 closest distance to " O   HOH Z 144 " =    1.736
peak=    5.409 closest distance to " CG  PRO A  54 " =    1.299
peak=    5.130 closest distance to " O   HOH Z 427 " =    2.341
peak=    5.120 closest distance to " CG  PRO A 213 " =    1.274
peak=    5.048 closest distance to " O   HOH Z  63 " =    1.734
peak=    5.006 closest distance to " O   HOH Z 423 " =    1.735
peak=    5.002 closest distance to " CB  SER A  63 " =    1.269
peak=    5.001 closest distance to " O   HOH Z 287 " =    1.979
peak=    4.941 closest distance to " O   HOH Z 232 " =    2.277
peak=    4.869 closest distance to " O   HOH Z 236 " =    1.472
peak=    4.835 closest distance to " O   HOH Z 417 " =    1.432
peak=    4.822 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.783 closest distance to " O   HOH Z 193 " =    1.895
peak=    4.762 closest distance to " O   HOH Z  78 " =    1.717
peak=    4.736 closest distance to " O   HOH Z   7 " =    1.438
peak=    4.687 closest distance to " CB  GLN A 223 " =    1.466
peak=    4.672 closest distance to " CB  ASN A 148 " =    1.453
peak=    4.645 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.641 closest distance to " O   HOH Z 298 " =    1.933
peak=    4.508 closest distance to " O   HOH Z 369 " =    2.138
peak=    4.504 closest distance to " CB  GLU A 128 " =    0.989
peak=    4.463 closest distance to " CB  ASN A 187 " =    1.281
peak=    4.443 closest distance to " O   HOH Z 380 " =    1.693
peak=    4.442 closest distance to " ND2 ASN A 187 " =    1.530
peak=    4.433 closest distance to " CG2 VAL A 257 " =    0.925
peak=    4.418 closest distance to " O   HOH Z 303 " =    2.279
peak=    4.416 closest distance to " CG  PRO A  90 " =    1.191
peak=    4.408 closest distance to " CB  SER A   3 " =    1.407
peak=    4.397 closest distance to " O   HOH Z 425 " =    1.394
peak=    4.367 closest distance to " O   HOH Z 368 " =    3.665
peak=    4.313 closest distance to " O   HOH Z 419 " =    2.225
peak=    4.311 closest distance to " CD  ARG A  66 " =    2.362
peak=    4.310 closest distance to " O   HOH Z   1 " =    1.648
peak=    4.290 closest distance to " O   HOH Z 217 " =    2.815
peak=    4.265 closest distance to " CB  GLU A 152 " =    1.328
peak=    4.244 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.232 closest distance to " C   PRO A 198 " =    1.476
peak=    4.200 closest distance to " O   HOH Z   9 " =    2.158
peak=    4.190 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.180 closest distance to " O   HOH Z 108 " =    1.487
peak=    4.162 closest distance to " CB  GLN A 183 " =    1.158
peak=    4.158 closest distance to " O   SER A  87 " =    2.142
peak=    4.127 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.108 closest distance to " O   HOH Z  44 " =    1.778
peak=    4.080 closest distance to " O   HOH Z 209 " =    2.307
peak=    4.065 closest distance to " O   HOH Z 146 " =    1.844
peak=    4.061 closest distance to " O   HOH Z 371 " =    1.723
peak=    4.055 closest distance to " CB  SER A 216 " =    0.747
peak=    4.045 closest distance to " O   HOH Z 261 " =    1.760
peak=    4.033 closest distance to " CB  ARG A  79 " =    1.264
peak=    4.030 closest distance to " CB  ARG A 139 " =    1.016
peak=    4.019 closest distance to " O   HOH Z 128 " =    1.989
peak=    4.018 closest distance to " O   HOH Z   1 " =    1.722
peak=    4.012 closest distance to " O   HOH Z 316 " =    3.014
peak=    3.991 closest distance to " O   HOH Z  61 " =    1.514
peak=    3.987 closest distance to " O   HOH Z 234 " =    3.705
peak=    3.985 closest distance to " O   HOH Z 352 " =    1.791
peak=    3.972 closest distance to " O   HOH Z  10 " =    1.759
peak=    3.960 closest distance to " O   HOH Z 250 " =    1.525
peak=    3.957 closest distance to " O   HOH Z 389 " =    1.885
peak=    3.957 closest distance to " CB  VAL A 265 " =    1.325
peak=    3.939 closest distance to " OG BSER A 164 " =    2.326
peak=    3.916 closest distance to " O   HOH Z   2 " =    1.637
peak=    3.908 closest distance to " CB  LEU A 228 " =    1.051
peak=    3.899 closest distance to " O   HOH Z  40 " =    2.256
peak=    3.895 closest distance to " O   HOH Z 112 " =    1.098
peak=    3.893 closest distance to " CG  GLN A  11 " =    2.020
peak=    3.892 closest distance to " O   HOH Z 124 " =    1.391
peak=    3.889 closest distance to " CA  ALA A 299 " =    0.865
peak=    3.889 closest distance to " CG  PRO A 243 " =    1.124
peak=    3.882 closest distance to " O   HOH Z 132 " =    2.295
peak=    3.876 closest distance to " OD1 ASN A  69 " =    2.639
peak=    3.848 closest distance to " CG  PRO A 280 " =    0.804
peak=    3.844 closest distance to " CB  TYR A 169 " =    0.740
peak=    3.826 closest distance to " O   HOH Z 425 " =    1.893
peak=    3.826 closest distance to " OD1BASN A 224 " =    2.183
peak=    3.816 closest distance to " CB  TRP A 179 " =    1.359
peak=    3.810 closest distance to " OD2 ASP A 286 " =    2.669
peak=    3.796 closest distance to " O   HOH Z 144 " =    2.259
peak=    3.792 closest distance to " O   HOH Z 394 " =    1.603
peak=    3.782 closest distance to " ND1 HIS A  86 " =    1.840
peak=    3.770 closest distance to " O   HOH Z  97 " =    1.897
peak=    3.766 closest distance to " O   HOH Z 222 " =    2.402
peak=    3.756 closest distance to " O   HOH Z 344 " =    3.009
peak=    3.750 closest distance to " O   HOH Z 366 " =    2.731
peak=    3.749 closest distance to " NH1AARG A 145 " =    1.128
peak=    3.738 closest distance to " O   HOH Z 368 " =    1.885
peak=    3.735 closest distance to " O   HOH Z 214 " =    2.081
peak=    3.717 closest distance to " CG2 THR A 221 " =    1.196
peak=    3.713 closest distance to " CA  ALA A  21 " =    1.159
peak=    3.713 closest distance to " CD BLYS A 290 " =    1.177
peak=    3.709 closest distance to " OG BSER A  99 " =    2.324
peak=    3.709 closest distance to " NE AARG A 275 " =    1.471
peak=    3.705 closest distance to " O   HOH Z 403 " =    1.366
peak=    3.702 closest distance to " CA  ASN A 215 " =    1.143
peak=    3.698 closest distance to " O   HOH Z 286 " =    2.297
peak=    3.692 closest distance to " O   HOH Z  21 " =    1.707
peak=    3.685 closest distance to " CG1 ILE A  33 " =    1.263
peak=    3.678 closest distance to " O   HOH Z 227 " =    1.854
peak=    3.669 closest distance to " N   PHE A 130 " =    1.231
peak=    3.669 closest distance to " O   HOH Z  68 " =    2.182
peak=    3.667 closest distance to " CB  ALA A  34 " =    1.128
peak=    3.667 closest distance to " O   HOH Z 158 " =    2.830
peak=    3.660 closest distance to " O   HOH Z  61 " =    1.646
peak=    3.649 closest distance to " O   HOH Z 327 " =    1.728
peak=    3.647 closest distance to " CD  PRO A 243 " =    1.589
peak=    3.644 closest distance to " NH1BARG A 145 " =    1.274
peak=    3.636 closest distance to " O   HOH Z 386 " =    2.971
peak=    3.625 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.615 closest distance to " CA  THR A 264 " =    0.836
peak=    3.605 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.605 closest distance to " CB  ARG A 190 " =    1.656
peak=    3.602 closest distance to " CB  LYS A 117 " =    1.166
peak=    3.601 closest distance to " N   GLN A 278 " =    1.061
peak=    3.601 closest distance to " O   HOH Z 405 " =    1.312
peak=    3.599 closest distance to " O   HOH Z 245 " =    1.308
peak=    3.595 closest distance to " O   HOH Z 291 " =    1.557
peak=    3.583 closest distance to " CB  GLU A 277 " =    3.490
peak=    3.567 closest distance to " CE1 TYR A 186 " =    1.341
peak=    3.565 closest distance to " CB  SER A  26 " =    1.601
peak=    3.557 closest distance to " CD  ARG A 159 " =    0.778
peak=    3.556 closest distance to " CB  THR A 157 " =    1.079
peak=    3.555 closest distance to " CB  ALA A  21 " =    1.834
peak=    3.549 closest distance to " O   HOH Z 426 " =    1.830
peak=    3.548 closest distance to " CB  ILE A 120 " =    1.259
peak=    3.542 closest distance to " O   HOH Z 244 " =    1.698
peak=    3.541 closest distance to " CB  ASN A  39 " =    0.795
peak=    3.528 closest distance to " O   HOH Z 357 " =    1.898
peak=    3.525 closest distance to " O   HOH Z 362 " =    2.051
peak=    3.523 closest distance to " CD1 ILE A 263 " =    1.402
peak=    3.517 closest distance to " O   HOH Z 119 " =    4.243
peak=    3.514 closest distance to " O   HOH Z 257 " =    2.220
peak=    3.513 closest distance to " NE2 GLN A  73 " =    3.566
peak=    3.509 closest distance to " CB  TRP A 266 " =    1.028
peak=    3.505 closest distance to " CB  SER A  62 " =    1.186
peak=    3.494 closest distance to " OG  SER A  62 " =    2.989
peak=    3.491 closest distance to " O   HOH Z 171 " =    2.740
peak=    3.481 closest distance to " O   HOH Z 139 " =    1.218
peak=    3.477 closest distance to " O   HOH Z 313 " =    1.753
peak=    3.475 closest distance to " O   HOH Z  88 " =    2.724
peak=    3.467 closest distance to " O   HOH Z  59 " =    1.999
peak=    3.467 closest distance to " O   HOH Z 213 " =    2.078
peak=    3.466 closest distance to " O   ASN A 209 " =    1.397
peak=    3.461 closest distance to " N   ASN A 127 " =    1.373
peak=    3.459 closest distance to " O   HOH Z 175 " =    2.058
peak=    3.459 closest distance to " O   HOH Z 392 " =    1.297
peak=    3.451 closest distance to " NH2BARG A 145 " =    2.120
peak=    3.448 closest distance to " O   HOH Z 128 " =    2.059
peak=    3.439 closest distance to " CB  LEU A 143 " =    1.115
peak=    3.438 closest distance to " O   HOH Z 151 " =    1.500
peak=    3.434 closest distance to " O   HOH Z 207 " =    1.637
peak=    3.431 closest distance to " O   HOH Z 281 " =    1.838
peak=    3.427 closest distance to " NZ  LYS A 117 " =    1.342
peak=    3.424 closest distance to " O   HOH Z 437 " =    1.921
peak=    3.424 closest distance to " O   HOH Z  44 " =    3.132
peak=    3.424 closest distance to " CH2 TRP A  92 " =    2.075
peak=    3.423 closest distance to " CA  ASP A 162 " =    1.121
peak=    3.421 closest distance to " O   HOH Z 298 " =    2.659
peak=    3.420 closest distance to " CA  GLY A 241 " =    3.683
peak=    3.419 closest distance to " CG1BVAL A  72 " =    1.358
peak=    3.418 closest distance to " O   HOH Z 371 " =    2.896
peak=    3.415 closest distance to " O   HOH Z 266 " =    3.074
peak=    3.415 closest distance to " N   TYR A  15 " =    0.830
peak=    3.415 closest distance to " N   ALA A   1 " =    2.161
peak=    3.414 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.411 closest distance to " CB  ALA A   1 " =    4.558
peak=    3.409 closest distance to " O   HOH Z  64 " =    1.965
peak=    3.409 closest distance to " O   HOH Z  93 " =    2.023
peak=    3.394 closest distance to " CB  THR A  31 " =    1.849
peak=    3.393 closest distance to " CA  ALA A 233 " =    1.130
peak=    3.383 closest distance to " O   HOH Z 423 " =    1.950
peak=    3.381 closest distance to " O   HOH Z 116 " =    2.829
peak=    3.374 closest distance to " CE AMET A  47 " =    1.294
peak=    3.373 closest distance to " CG  GLN A  89 " =    1.458
peak=    3.367 closest distance to " CB  ALA A 114 " =    1.139
peak=    3.364 closest distance to " O   HOH Z   9 " =    2.085
peak=    3.361 closest distance to " NE2 GLN A  58 " =    3.476
peak=    3.358 closest distance to " CD2 LEU A 255 " =    1.089
peak=    3.355 closest distance to " O   HOH Z 352 " =    1.479
peak=    3.352 closest distance to " CA  PHE A 283 " =    1.376
peak=    3.352 closest distance to " O   HOH Z 432 " =    1.913
peak=    3.350 closest distance to " O   HOH Z 189 " =    1.835
peak=    3.347 closest distance to " O   HOH Z  50 " =    1.666
peak=    3.346 closest distance to " N   SER A 134 " =    1.324
peak=    3.343 closest distance to " O   HOH Z 128 " =    2.094
peak=    3.340 closest distance to " O   HOH Z 336 " =    1.872
peak=    3.339 closest distance to " O   HOH Z 147 " =    1.713
peak=    3.337 closest distance to " O   HOH Z 180 " =    2.074
peak=    3.335 closest distance to " O   HOH Z 261 " =    2.273
peak=    3.334 closest distance to " O   HOH Z 422 " =    2.705
peak=    3.330 closest distance to " O   HOH Z 374 " =    2.603
peak=    3.328 closest distance to " CG  LEU A 167 " =    1.217
peak=    3.328 closest distance to " CA  ILE A 234 " =    1.000
peak=    3.327 closest distance to " O   HOH Z 345 " =    1.747
peak=    3.323 closest distance to " CB  GLN A  88 " =    1.273
peak=    3.321 closest distance to " O   HOH Z 329 " =    3.558
peak=    3.319 closest distance to " O   HOH Z 195 " =    1.347
peak=    3.318 closest distance to " CG  GLU A 277 " =    2.074
peak=    3.318 closest distance to " NZ  LYS A  76 " =    1.544
peak=    3.314 closest distance to " O   HOH Z  88 " =    2.961
peak=    3.312 closest distance to " N   GLU A   2 " =    1.345
peak=    3.310 closest distance to " O   HOH Z 282 " =    2.335
peak=    3.308 closest distance to " O   HOH Z 263 " =    2.372
peak=    3.302 closest distance to " O   HOH Z 334 " =    2.863
peak=    3.300 closest distance to " O   HOH Z  49 " =    1.244
peak=    3.299 closest distance to " O   HOH Z  73 " =    1.758
peak=    3.295 closest distance to " O   HOH Z  30 " =    1.731
peak=    3.291 closest distance to " O   HOH Z  17 " =    2.075
peak=    3.289 closest distance to " CG1 ILE A 151 " =    1.012
peak=    3.286 closest distance to " O   HOH Z 217 " =    1.667
peak=    3.284 closest distance to " O   HOH Z 345 " =    3.389
peak=    3.281 closest distance to " N   GLY A 241 " =    1.486
peak=    3.280 closest distance to " CB  SER A 276 " =    1.246
peak=    3.278 closest distance to " O  BHOH Z  74 " =    1.512
peak=    3.276 closest distance to " O   HOH Z 359 " =    1.374
peak=    3.264 closest distance to " O   HOH Z 273 " =    2.809
peak=    3.260 closest distance to " O   HOH Z 271 " =    2.239
peak=    3.259 closest distance to " N   ARG A 156 " =    1.325
peak=    3.257 closest distance to " O   HOH Z   6 " =    1.985
peak=    3.256 closest distance to " O   HOH Z 285 " =    1.730
peak=    3.255 closest distance to " O   HOH Z 305 " =    3.534
peak=    3.253 closest distance to " CA  SER A  87 " =    0.996
peak=    3.252 closest distance to " CB  ASP A 124 " =    0.888
peak=    3.252 closest distance to " O   HOH Z  47 " =    1.840
peak=    3.250 closest distance to " CB  ARG A 138 " =    0.939
peak=    3.249 closest distance to " CB  ASP A 132 " =    4.042
peak=    3.249 closest distance to " O   HOH Z 193 " =    1.566
peak=    3.248 closest distance to " O   HOH Z  89 " =    2.148
peak=    3.248 closest distance to " CD2 TRP A 179 " =    1.305
peak=    3.246 closest distance to " CB  MET A  40 " =    0.943
peak=    3.243 closest distance to " O   GLY A 302 " =    1.583
peak=    3.242 closest distance to " O   ALA A   1 " =    1.511
peak=    3.241 closest distance to " CB  TYR A 116 " =    0.917
peak=    3.238 closest distance to " O   HOH Z 108 " =    1.938
peak=    3.237 closest distance to " O   HOH Z  71 " =    2.025
peak=    3.235 closest distance to " O   HOH Z  32 " =    1.861
peak=    3.232 closest distance to " CB  VAL A 202 " =    1.608
peak=    3.230 closest distance to " OH  TYR A 116 " =    1.064
peak=    3.229 closest distance to " CB  TYR A  30 " =    1.079
peak=    3.226 closest distance to " O   HOH Z 139 " =    2.364
peak=    3.224 closest distance to " O   HOH Z 193 " =    2.007
peak=    3.216 closest distance to " O   HOH Z 289 " =    1.636
peak=    3.215 closest distance to " NE2 GLN A 278 " =    3.419
peak=    3.215 closest distance to " CB  ASN A 142 " =    0.913
peak=    3.213 closest distance to " CD2 LEU A 297 " =    1.004
peak=    3.209 closest distance to " O   HOH Z 173 " =    1.953
peak=    3.209 closest distance to " CG2 ILE A 120 " =    1.084
peak=    3.206 closest distance to " O   HOH Z  43 " =    2.038
peak=    3.205 closest distance to " O   HOH Z  49 " =    1.847
peak=    3.200 closest distance to " O   HOH Z 291 " =    1.980
peak=    3.198 closest distance to " O   HOH Z  40 " =    2.998
peak=    3.196 closest distance to " CB  LYS A 290 " =    1.375
peak=    3.191 closest distance to " O   ARG A 195 " =    1.720
peak=    3.190 closest distance to " O   HOH Z 412 " =    2.158
peak=    3.187 closest distance to " O   HOH Z  54 " =    1.502
peak=    3.187 closest distance to " CD  LYS A 166 " =    1.352
peak=    3.179 closest distance to " CB  GLU A 277 " =    1.012
peak=    3.178 closest distance to " O   HOH Z  59 " =    1.498
peak=    3.178 closest distance to " CB  LEU A 300 " =    0.969
peak=    3.175 closest distance to " OG  SER A  22 " =    2.757
peak=    3.166 closest distance to " CG BARG A 102 " =    1.828
peak=    3.166 closest distance to " O   HOH Z 258 " =    1.720
peak=    3.165 closest distance to " N   SER A  97 " =    0.865
peak=    3.162 closest distance to " CA  ALA A  51 " =    1.048
peak=    3.159 closest distance to " O   HOH Z 438 " =    2.114
peak=    3.157 closest distance to " O   HOH Z 152 " =    2.309
peak=    3.155 closest distance to " O   HOH Z 409 " =    2.269
peak=    3.152 closest distance to " O   HOH Z 383 " =    1.830
peak=    3.149 closest distance to " CA  ALA A  84 " =    1.435
peak=    3.147 closest distance to " CA  MET A  40 " =    1.092
peak=    3.146 closest distance to " O   HOH Z  66 " =    2.088
peak=    3.146 closest distance to " O   GLY A 147 " =    1.368
peak=    3.144 closest distance to " CB  ARG A 102 " =    0.756
peak=    3.143 closest distance to " CG1BVAL A  72 " =    1.417
peak=    3.143 closest distance to " CD2 HIS A  81 " =    1.224
peak=    3.138 closest distance to " O   HOH Z 166 " =    1.418
peak=    3.133 closest distance to " CB  PRO A 243 " =    1.134
peak=    3.129 closest distance to " N   ALA A   1 " =    3.015
peak=    3.120 closest distance to " CE3 TRP A  85 " =    0.912
peak=    3.114 closest distance to " O   HOH Z 251 " =    1.620
peak=    3.113 closest distance to " O   HOH Z 106 " =    2.605
peak=    3.112 closest distance to " CG  GLN A 278 " =    1.249
peak=    3.111 closest distance to " O   HOH Z 188 " =    1.969
peak=    3.104 closest distance to " CD1 ILE A 106 " =    0.935
peak=    3.104 closest distance to " CB  ALA A 114 " =    1.430
peak=    3.100 closest distance to " CB  GLU A 152 " =    1.378
peak=    3.098 closest distance to " O   HOH Z 172 " =    2.706
peak=    3.085 closest distance to " O   HOH Z 189 " =    1.999
peak=    3.081 closest distance to " O   HOH Z 375 " =    1.034
peak=    3.080 closest distance to " CG2BVAL A  41 " =    0.769
peak=    3.071 closest distance to " O   HOH Z 213 " =    1.919
peak=    3.071 closest distance to " O   HOH Z 334 " =    1.283
peak=    3.069 closest distance to " O   HOH Z 302 " =    1.509
peak=    3.067 closest distance to " CA  ILE A  33 " =    1.428
peak=    3.060 closest distance to " CA  ALA A 158 " =    1.072
peak=    3.053 closest distance to " O   HOH Z 263 " =    1.754
peak=    3.043 closest distance to " CB  ARG A 190 " =    1.086
peak=    3.037 closest distance to " CG  GLN A 144 " =    1.037
peak=    3.031 closest distance to " CA  VAL A 126 " =    1.111

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.717 - 5.716
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.717 - 5.716

peak=   -4.631 closest distance to " O   HOH Z 290 " =    1.102
peak=   -4.488 closest distance to " C   HIS A 108 " =    1.168
peak=   -4.448 closest distance to " CB  PRO A 243 " =    2.558
peak=   -4.377 closest distance to " O   HOH Z  65 " =    0.967
peak=   -4.335 closest distance to " CD  ARG A  14 " =    3.252
peak=   -4.286 closest distance to " CD1 LEU A 255 " =    2.932
peak=   -4.248 closest distance to " O   PRO A 198 " =    1.325
peak=   -4.224 closest distance to " O   HOH Z 438 " =    0.956
peak=   -4.211 closest distance to " O   HOH Z 377 " =    1.981
peak=   -4.140 closest distance to " CA  GLY A  98 " =    1.798
peak=   -4.136 closest distance to " CD  ARG A 156 " =    1.976
peak=   -4.117 closest distance to " N   GLN A  58 " =    1.682
peak=   -4.117 closest distance to " O   HOH Z 372 " =    2.545
peak=   -4.095 closest distance to " O   HOH Z 266 " =    4.416
peak=   -4.043 closest distance to " CE1 PHE A  59 " =    1.435
peak=   -3.981 closest distance to " O   HOH Z 407 " =    3.170
peak=   -3.975 closest distance to " O   ARG A 145 " =    1.491
peak=   -3.972 closest distance to " O   SER A 135 " =    1.451
peak=   -3.936 closest distance to " CG  PHE A 283 " =    2.606
peak=   -3.920 closest distance to " O   PRO A 243 " =    2.496
peak=   -3.875 closest distance to " ND2 ASN A  45 " =    1.024
peak=   -3.869 closest distance to " O   HOH Z 313 " =    1.960
peak=   -3.858 closest distance to " O   HOH Z 351 " =    1.550
peak=   -3.857 closest distance to " CG  ASP A 231 " =    0.771
peak=   -3.843 closest distance to " OG BSER A 134 " =    1.337
peak=   -3.843 closest distance to " O   VAL A  67 " =    2.675
peak=   -3.839 closest distance to " CE3 TRP A 123 " =    1.343
peak=   -3.829 closest distance to " CG1 VAL A 112 " =    2.968
peak=   -3.822 closest distance to " CG  GLN A 223 " =    1.624
peak=   -3.815 closest distance to " O   VAL A 153 " =    2.334
peak=   -3.808 closest distance to " CE2 PHE A 218 " =    2.454
peak=   -3.808 closest distance to " OD1 ASP A 191 " =    1.510
peak=   -3.806 closest distance to " C   ALA A 158 " =    1.404
peak=   -3.798 closest distance to " O   HOH Z 231 " =    2.006
peak=   -3.793 closest distance to " CB  TYR A  15 " =    2.142
peak=   -3.771 closest distance to " O   HOH Z 185 " =    1.992
peak=   -3.765 closest distance to " O   HOH Z  13 " =    1.336
peak=   -3.744 closest distance to " O   VAL A  67 " =    2.572
peak=   -3.722 closest distance to " OD2 ASP A 191 " =    1.481
peak=   -3.714 closest distance to " O   HOH Z 388 " =    2.042
peak=   -3.699 closest distance to " NH1AARG A 275 " =    1.744
peak=   -3.692 closest distance to " O   HOH Z  43 " =    1.816
peak=   -3.682 closest distance to " OE1 GLN A  88 " =    1.130
peak=   -3.669 closest distance to " O   HOH Z  52 " =    1.320
peak=   -3.654 closest distance to " OD1 ASN A 187 " =    1.534
peak=   -3.650 closest distance to " O   HOH Z 198 " =    1.876
peak=   -3.647 closest distance to " NH2 ARG A  79 " =    1.895
peak=   -3.642 closest distance to " O   HOH Z 250 " =    1.404
peak=   -3.638 closest distance to " CB  ALA A 291 " =    2.116
peak=   -3.633 closest distance to " C   LYS A  76 " =    1.643
peak=   -3.630 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.623 closest distance to " CB  ALA A 248 " =    1.957
peak=   -3.623 closest distance to " O   SER A  22 " =    2.530
peak=   -3.622 closest distance to " C   ASN A 285 " =    2.337
peak=   -3.620 closest distance to " O   ALA A 161 " =    1.520
peak=   -3.619 closest distance to " O   HOH Z  93 " =    2.046
peak=   -3.611 closest distance to " OD1 ASP A 191 " =    1.835
peak=   -3.610 closest distance to " CA  GLY A 133 " =    2.020
peak=   -3.610 closest distance to " CE  LYS A  76 " =    2.905
peak=   -3.587 closest distance to " O   HOH Z 298 " =    1.221
peak=   -3.579 closest distance to " CD1 LEU A 101 " =    2.268
peak=   -3.567 closest distance to " N   GLN A 122 " =    1.472
peak=   -3.560 closest distance to " CA  GLY A 203 " =    2.171
peak=   -3.555 closest distance to " O   HOH Z  60 " =    2.320
peak=   -3.548 closest distance to " CB  ASN A  39 " =    2.226
peak=   -3.546 closest distance to " O   HOH Z 148 " =    1.816
peak=   -3.540 closest distance to " O   HOH Z 152 " =    4.750
peak=   -3.539 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.536 closest distance to " CB  CYS A 254 " =    2.164
peak=   -3.536 closest distance to " O   HOH Z  11 " =    1.852
peak=   -3.522 closest distance to " O   SER A  95 " =    1.369
peak=   -3.519 closest distance to " CZ3 TRP A 123 " =    1.787
peak=   -3.517 closest distance to " NE2 GLN A 278 " =    1.636
peak=   -3.510 closest distance to " CB  ILE A  33 " =    2.832
peak=   -3.508 closest distance to " O   PRO A 198 " =    1.215
peak=   -3.507 closest distance to " N   THR A 157 " =    1.482
peak=   -3.505 closest distance to " O   HOH Z 389 " =    1.773
peak=   -3.505 closest distance to " O   HOH Z 359 " =    3.336
peak=   -3.502 closest distance to " OD2 ASP A 171 " =    2.018
peak=   -3.500 closest distance to " O   HOH Z 166 " =    1.237
peak=   -3.480 closest distance to " O   ASP A 162 " =    2.198
peak=   -3.474 closest distance to " CD2 TYR A 293 " =    1.890
peak=   -3.466 closest distance to " O   VAL A 189 " =    2.399
peak=   -3.452 closest distance to " O   HOH Z  63 " =    2.386
peak=   -3.448 closest distance to " OD1 ASN A 148 " =    1.710
peak=   -3.446 closest distance to " CE  LYS A 166 " =    1.158
peak=   -3.445 closest distance to " CE  MET A  93 " =    1.123
peak=   -3.442 closest distance to " CG  GLN A  58 " =    1.303
peak=   -3.435 closest distance to " O   HOH Z  60 " =    1.977
peak=   -3.426 closest distance to " CA  ASP A  27 " =    2.406
peak=   -3.425 closest distance to " CG  GLU A 152 " =    1.158
peak=   -3.422 closest distance to " CB  CYS A 201 " =    2.494
peak=   -3.421 closest distance to " CA  GLY A  57 " =    2.040
peak=   -3.420 closest distance to " CE3 TRP A 274 " =    2.424
peak=   -3.412 closest distance to " ND2 ASN A 187 " =    1.368
peak=   -3.406 closest distance to " ND2 ASN A  45 " =    1.759
peak=   -3.404 closest distance to " O   HOH Z 385 " =    2.106
peak=   -3.402 closest distance to " O   HOH Z  24 " =    1.224
peak=   -3.401 closest distance to " O   ALA A  34 " =    2.829
peak=   -3.398 closest distance to " CB  ALA A   7 " =    1.971
peak=   -3.392 closest distance to " O   HOH Z 211 " =    1.565
peak=   -3.390 closest distance to " O   HOH Z  90 " =    2.374
peak=   -3.388 closest distance to " CE  MET A 105 " =    2.242
peak=   -3.386 closest distance to " O   HOH Z 377 " =    0.790
peak=   -3.383 closest distance to " OG  SER A  87 " =    1.237
peak=   -3.382 closest distance to " NE  ARG A  36 " =    1.875
peak=   -3.380 closest distance to " OG1 THR A 246 " =    1.519
peak=   -3.378 closest distance to " O   ALA A  51 " =    1.406
peak=   -3.376 closest distance to " OG  SER A  97 " =    2.141
peak=   -3.372 closest distance to " O   MET A  40 " =    2.732
peak=   -3.362 closest distance to " C   ALA A 114 " =    2.324
peak=   -3.360 closest distance to " OG BSER A 134 " =    1.541
peak=   -3.358 closest distance to " ND2 ASN A 252 " =    1.694
peak=   -3.352 closest distance to " CZ  TYR A 169 " =    1.532
peak=   -3.351 closest distance to " C   LEU A 143 " =    1.236
peak=   -3.350 closest distance to " O   HOH Z 345 " =    1.969
peak=   -3.349 closest distance to " CB  PRO A 163 " =    2.547
peak=   -3.341 closest distance to " CD1 PHE A  59 " =    1.937
peak=   -3.338 closest distance to " O   HOH Z 266 " =    4.191
peak=   -3.338 closest distance to " O   VAL A 174 " =    2.168
peak=   -3.336 closest distance to " O   HOH Z 369 " =    2.138
peak=   -3.333 closest distance to " O   HOH Z 131 " =    4.048
peak=   -3.329 closest distance to " OD1 ASP A 171 " =    1.603
peak=   -3.327 closest distance to " O   HOH Z 191 " =    5.437
peak=   -3.327 closest distance to " O   TRP A  70 " =    1.473
peak=   -3.325 closest distance to " CE1 TYR A 169 " =    2.517
peak=   -3.323 closest distance to " CB  ALA A 161 " =    2.534
peak=   -3.320 closest distance to " O   TYR A 247 " =    2.804
peak=   -3.318 closest distance to " OD2 ASP A  27 " =    1.549
peak=   -3.313 closest distance to " CG2 VAL A 232 " =    2.012
peak=   -3.306 closest distance to " O   HOH Z 126 " =    1.868
peak=   -3.302 closest distance to " O   HOH Z 393 " =    3.217
peak=   -3.302 closest distance to " N   ALA A  43 " =    2.338
peak=   -3.298 closest distance to " O   HOH Z 298 " =    2.476
peak=   -3.295 closest distance to " O   PRO A 163 " =    1.886
peak=   -3.294 closest distance to " O   HOH Z 348 " =    1.797
peak=   -3.292 closest distance to " N   SER A 212 " =    1.860
peak=   -3.291 closest distance to " NE2 GLN A 194 " =    2.692
peak=   -3.290 closest distance to " C   LEU A 222 " =    0.717
peak=   -3.288 closest distance to " CE2 TYR A  30 " =    2.719
peak=   -3.286 closest distance to " O   HOH Z 384 " =    2.802
peak=   -3.281 closest distance to " O   HOH Z 351 " =    1.708
peak=   -3.276 closest distance to " CA  SER A 146 " =    2.294
peak=   -3.276 closest distance to " O   HOH Z 102 " =    1.639
peak=   -3.274 closest distance to " O   PHE A 218 " =    1.496
peak=   -3.274 closest distance to " NE2 GLN A  58 " =    2.980
peak=   -3.271 closest distance to " O   HOH Z 409 " =    5.716
peak=   -3.265 closest distance to " NH2AARG A 275 " =    5.216
peak=   -3.265 closest distance to " CG1 VAL A 197 " =    2.100
peak=   -3.260 closest distance to " O   HOH Z 134 " =    2.843
peak=   -3.258 closest distance to " OG1 THR A 178 " =    1.141
peak=   -3.254 closest distance to " OXT GLY A 302 " =    2.756
peak=   -3.251 closest distance to " CG  PRO A 243 " =    1.627
peak=   -3.249 closest distance to " CD  ARG A 139 " =    1.537
peak=   -3.244 closest distance to " O   SER A   3 " =    1.160
peak=   -3.244 closest distance to " CB  ASP A 132 " =    2.218
peak=   -3.239 closest distance to " C   PRO A  90 " =    1.508
peak=   -3.236 closest distance to " O   HOH Z 213 " =    1.221
peak=   -3.232 closest distance to " CE2 PHE A 204 " =    1.911
peak=   -3.230 closest distance to " CD  GLU A 277 " =    1.105
peak=   -3.229 closest distance to " O   HOH Z 263 " =    2.872
peak=   -3.229 closest distance to " CD2 PHE A 225 " =    1.124
peak=   -3.226 closest distance to " O   HOH Z 103 " =    1.784
peak=   -3.223 closest distance to " CB  TRP A  85 " =    2.412
peak=   -3.219 closest distance to " O   GLN A 240 " =    1.941
peak=   -3.219 closest distance to " O   HOH Z  51 " =    1.044
peak=   -3.218 closest distance to " OE1 GLU A 277 " =    2.188
peak=   -3.217 closest distance to " CB  ASP A 132 " =    2.292
peak=   -3.215 closest distance to " CE3 TRP A 274 " =    0.970
peak=   -3.213 closest distance to " O   HOH Z 137 " =    1.487
peak=   -3.205 closest distance to " O   ALA A   7 " =    1.614
peak=   -3.205 closest distance to " O   HOH Z 209 " =    2.516
peak=   -3.204 closest distance to " O   HOH Z 300 " =    2.010
peak=   -3.200 closest distance to " CD1 LEU A 228 " =    2.139
peak=   -3.196 closest distance to " O   GLN A  11 " =    1.635
peak=   -3.192 closest distance to " NH2 ARG A 219 " =    1.767
peak=   -3.191 closest distance to " O   HOH Z 309 " =    2.425
peak=   -3.190 closest distance to " O   HOH Z 326 " =    1.616
peak=   -3.188 closest distance to " O   HOH Z 281 " =    3.000
peak=   -3.182 closest distance to " ND2 ASN A  69 " =    1.547
peak=   -3.172 closest distance to " ND2 ASN A 249 " =    2.359
peak=   -3.171 closest distance to " N   ALA A 248 " =    1.500
peak=   -3.171 closest distance to " O   HOH Z  88 " =    1.820
peak=   -3.166 closest distance to " O   HOH Z 236 " =    1.800
peak=   -3.162 closest distance to " ND2 ASN A 285 " =    2.034
peak=   -3.160 closest distance to " CB  PHE A 192 " =    1.654
peak=   -3.159 closest distance to " ND2 ASN A  39 " =    1.558
peak=   -3.159 closest distance to " O   ARG A  66 " =    1.241
peak=   -3.154 closest distance to " OE1 GLN A 223 " =    2.041
peak=   -3.151 closest distance to " O   GLY A  80 " =    2.432
peak=   -3.142 closest distance to " N   VAL A  72 " =    1.517
peak=   -3.138 closest distance to " O   HOH Z   9 " =    2.955
peak=   -3.137 closest distance to " O   HOH Z  97 " =    1.655
peak=   -3.135 closest distance to " O   HOH Z 234 " =    3.892
peak=   -3.119 closest distance to " CD2 LEU A 237 " =    2.469
peak=   -3.105 closest distance to " O   HOH Z 111 " =    2.188
peak=   -3.090 closest distance to " O   HOH Z 210 " =    0.838
peak=   -3.088 closest distance to " O   HOH Z  28 " =    1.879
peak=   -3.079 closest distance to " O   HOH Z 114 " =    0.773
peak=   -3.075 closest distance to " O   HOH Z 198 " =    1.585
peak=   -3.044 closest distance to " CD1 ILE A 239 " =    2.128
peak=   -3.034 closest distance to " O   ILE A  49 " =    1.689
peak=   -3.025 closest distance to " CZ  ARG A  66 " =    0.815
peak=   -3.021 closest distance to " CG  PRO A 163 " =    2.598
peak=   -3.005 closest distance to " CD  GLN A 223 " =    1.404

================= 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    :  0.4315 0.4295   6.242234e+00   6.235796e+00
   1_bss:  0.4188 0.4169   6.232814e+00   6.217722e+00
   1_xyz:  0.2896 0.3215   5.950507e+00   6.024643e+00
   1_adp:  0.2627 0.3388   5.903057e+00   6.055714e+00
   1_occ:  0.2624 0.3391   5.902169e+00   6.055213e+00
   2_bss:  0.2604 0.3357   5.894916e+00   6.047411e+00
   2_xyz:  0.1912 0.2451   5.608116e+00   5.796034e+00
   2_adp:  0.1713 0.2219   5.511512e+00   5.711186e+00
   2_occ:  0.1710 0.2216   5.510363e+00   5.710039e+00
   3_bss:  0.1707 0.2204   5.505421e+00   5.704467e+00
   3_xyz:  0.1329 0.1797   5.278330e+00   5.507359e+00
   3_adp:  0.1246 0.1720   5.226291e+00   5.461623e+00
   3_occ:  0.1245 0.1718   5.225567e+00   5.460619e+00
   4_bss:  0.1245 0.1715   5.225615e+00   5.459965e+00
   4_xyz:  0.1123 0.1597   5.145588e+00   5.396550e+00
   4_adp:  0.1101 0.1573   5.130821e+00   5.384234e+00
   4_occ:  0.1100 0.1572   5.130504e+00   5.383834e+00
   5_bss:  0.1100 0.1571   5.130269e+00   5.383609e+00
   5_xyz:  0.1099 0.1560   5.125217e+00   5.373864e+00
   5_adp:  0.1100 0.1550   5.122888e+00   5.369884e+00
   5_occ:  0.1100 0.1550   5.122571e+00   5.369580e+00
   5_bss:  0.1100 0.1550   5.122625e+00   5.369603e+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:  0.343  26.501  -3.295   2.810   0.373   0.000   0.000   0.000
   1_xyz:  0.343  26.501  -3.295   2.810   0.373   0.000   0.000   0.000
   1_adp:  0.343  26.501  -3.295   2.810   0.373   0.000   0.000   0.000
   1_occ:  0.343  26.501  -3.295   2.810   0.373   0.000   0.000   0.000
   2_bss:  0.329  38.952  -2.033  -0.257  -0.561  -0.000  -0.000  -0.000
   2_xyz:  0.329  38.952  -2.033  -0.257  -0.561  -0.000  -0.000  -0.000
   2_adp:  0.329  38.952  -2.033  -0.257  -0.561  -0.000  -0.000  -0.000
   2_occ:  0.329  38.952  -2.033  -0.257  -0.561  -0.000  -0.000  -0.000
   3_bss:  0.324  38.952  -1.900  -1.432  -0.867  -0.000  -0.000  -0.000
   3_xyz:  0.324  38.952  -1.900  -1.432  -0.867  -0.000  -0.000  -0.000
   3_adp:  0.324  38.952  -1.900  -1.432  -0.867  -0.000  -0.000  -0.000
   3_occ:  0.324  38.952  -1.900  -1.432  -0.867  -0.000  -0.000  -0.000
   4_bss:  0.317  40.201  -2.255  -2.211  -1.311  -0.000  -0.000  -0.000
   4_xyz:  0.317  40.201  -2.255  -2.211  -1.311  -0.000  -0.000  -0.000
   4_adp:  0.317  40.201  -2.255  -2.211  -1.311  -0.000  -0.000  -0.000
   4_occ:  0.317  40.201  -2.255  -2.211  -1.311  -0.000  -0.000  -0.000
   5_bss:  0.319  40.950  -2.198  -2.295  -1.306  -0.000  -0.000  -0.000
   5_xyz:  0.319  40.950  -2.198  -2.295  -1.306  -0.000  -0.000  -0.000
   5_adp:  0.319  40.950  -2.198  -2.295  -1.306  -0.000  -0.000  -0.000
   5_occ:  0.319  40.950  -2.198  -2.295  -1.306  -0.000  -0.000  -0.000
   5_bss:  0.320  40.912  -2.065  -2.234  -1.190  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.881 0.5236  0.7099    58988.669
   1_bss:  48.535 0.5385  0.7279    54653.107
   1_xyz:  33.444 0.7206  0.9245    28645.330
   1_adp:  35.451 0.6963  0.8958    31323.420
   1_occ:  35.452 0.6963  0.8948    31302.738
   2_bss:  34.824 0.7033  0.8777    30341.521
   2_xyz:  24.494 0.8160  0.9834    15392.145
   2_adp:  21.357 0.8489  1.0003    12543.896
   2_occ:  21.316 0.8493  1.0000    12496.797
   3_bss:  21.136 0.8509  0.9847    12279.059
   3_xyz:  16.581 0.8926  1.0064     8008.907
   3_adp:  15.513 0.9023  1.0051     7452.714
   3_occ:  15.493 0.9025  1.0050     7429.948
   4_bss:  15.471 0.9026  0.9860     7429.124
   4_xyz:  14.148 0.9135  0.9919     6432.778
   4_adp:  13.861 0.9160  0.9894     6274.710
   4_occ:  13.852 0.9161  0.9894     6266.693
   5_bss:  13.846 0.9161  0.9893     6266.024
   5_xyz:  13.627 0.9180  0.9889     6149.093
   5_adp:  13.513 0.9190  0.9857     6099.242
   5_occ:  13.508 0.9190  0.9857     6090.663
   5_bss:  13.509 0.9190  0.9884     6092.967
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7452e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7452e-01
   1_xyz:   1.530  0.012  0.101 15.546  0.006  4.104   1.2460e-01
   1_adp:   1.530  0.012  0.101 15.546  0.006  4.104   1.2460e-01
   1_occ:   1.530  0.012  0.101 15.546  0.006  4.104   1.2460e-01
   2_bss:   1.530  0.012  0.101 15.546  0.006  4.104   1.2460e-01
   2_xyz:   1.153  0.007  0.079 14.504  0.005  4.107   7.0479e-02
   2_adp:   1.153  0.007  0.079 14.504  0.005  4.107   7.0479e-02
   2_occ:   1.153  0.007  0.079 14.504  0.005  4.107   7.0479e-02
   3_bss:   1.153  0.007  0.079 14.504  0.005  4.107   7.0479e-02
   3_xyz:   1.004  0.006  0.070 14.617  0.004  4.109   5.9241e-02
   3_adp:   1.004  0.006  0.070 14.617  0.004  4.109   5.9241e-02
   3_occ:   1.004  0.006  0.070 14.617  0.004  4.109   5.9241e-02
   4_bss:   1.004  0.006  0.070 14.617  0.004  4.109   5.9241e-02
   4_xyz:   1.069  0.007  0.076 14.829  0.005  4.108   6.6647e-02
   4_adp:   1.069  0.007  0.076 14.829  0.005  4.108   6.6647e-02
   4_occ:   1.069  0.007  0.076 14.829  0.005  4.108   6.6647e-02
   5_bss:   1.069  0.007  0.076 14.829  0.005  4.108   6.6647e-02
   5_xyz:   0.944  0.006  0.069 14.456  0.004  4.108   5.4115e-02
   5_adp:   0.944  0.006  0.069 14.456  0.004  4.108   5.4115e-02
   5_occ:   0.944  0.006  0.069 14.456  0.004  4.108   5.4115e-02
   5_bss:   0.944  0.006  0.069 14.456  0.004  4.108   5.4115e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.767   2.3795e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.767   2.3795e-01
   1_xyz:   9.045  0.062  0.453 86.437  0.036  2.100   1.1905e-01
   1_adp:   9.045  0.062  0.453 86.437  0.036  2.100   1.1905e-01
   1_occ:   9.045  0.062  0.453 86.437  0.036  2.100   1.1905e-01
   2_bss:   9.045  0.062  0.453 86.437  0.036  2.100   1.1905e-01
   2_xyz:   7.495  0.033  0.242 83.115  0.032  2.296   7.0540e-02
   2_adp:   7.495  0.033  0.242 83.115  0.032  2.296   7.0540e-02
   2_occ:   7.495  0.033  0.242 83.115  0.032  2.296   7.0540e-02
   3_bss:   7.495  0.033  0.242 83.115  0.032  2.296   7.0540e-02
   3_xyz:   6.914  0.044  0.211 83.337  0.034  2.293   6.2395e-02
   3_adp:   6.914  0.044  0.211 83.337  0.034  2.293   6.2395e-02
   3_occ:   6.914  0.044  0.211 83.337  0.034  2.293   6.2395e-02
   4_bss:   6.914  0.044  0.211 83.337  0.034  2.293   6.2395e-02
   4_xyz:   6.560  0.034  0.233 84.421  0.038  2.268   8.1985e-02
   4_adp:   6.560  0.034  0.233 84.421  0.038  2.268   8.1985e-02
   4_occ:   6.560  0.034  0.233 84.421  0.038  2.268   8.1985e-02
   5_bss:   6.560  0.034  0.233 84.421  0.038  2.268   8.1985e-02
   5_xyz:   6.457  0.033  0.204 84.687  0.041  2.318   3.9739e-02
   5_adp:   6.457  0.033  0.204 84.687  0.041  2.318   3.9739e-02
   5_occ:   6.457  0.033  0.204 84.687  0.041  2.318   3.9739e-02
   5_bss:   6.457  0.033  0.204 84.687  0.041  2.318   3.9739e-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:  95.68   0.00  18.09  78.56   0.00  14.12  95.68   2.34  39.73
   1_occ:  95.68   0.00  18.09  78.56   0.00  14.12  95.68   2.34  39.73
   2_bss:  95.68   0.00  18.09  78.56   0.00  14.12  95.68   2.34  39.73
   2_xyz:  95.68   0.00  18.09  78.56   0.00  14.12  95.68   2.34  39.73
   2_adp:  88.65   0.00  17.11  79.85   0.00  13.05  88.65   5.45  39.20
   2_occ:  88.65   0.00  17.11  79.85   0.00  13.05  88.65   5.45  39.20
   3_bss:  88.65   0.00  17.11  79.85   0.00  13.05  88.65   5.45  39.20
   3_xyz:  88.65   0.00  17.11  79.85   0.00  13.05  88.65   5.45  39.20
   3_adp:  85.73   0.82  17.02  84.54   0.82  12.70  85.73   5.78  40.56
   3_occ:  85.73   0.82  17.02  84.54   0.82  12.70  85.73   5.78  40.56
   4_bss:  85.73   0.82  17.02  84.54   0.82  12.70  85.73   5.78  40.56
   4_xyz:  85.73   0.82  17.02  84.54   0.82  12.70  85.73   5.78  40.56
   4_adp:  89.65   0.54  16.84  89.65   0.54  12.59  85.65   6.32  39.98
   4_occ:  89.65   0.54  16.84  89.65   0.54  12.59  85.65   6.32  39.98
   5_bss:  89.65   0.54  16.84  89.65   0.54  12.59  85.65   6.32  39.98
   5_xyz:  89.65   0.54  16.84  89.65   0.54  12.59  85.65   6.32  39.98
   5_adp:  90.10   0.91  16.52  90.10   0.91  12.47  82.82   6.27  38.58
   5_occ:  90.10   0.91  16.52  90.10   0.91  12.47  82.82   6.27  38.58
   5_bss:  90.07   0.88  16.49  90.07   0.88  12.44  82.79   6.24  38.55
------------------------------------------------------------------------
 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:    1.774    0.032    0.435
   1_adp:    1.774    0.032    0.435
   1_occ:    1.774    0.032    0.435
   2_bss:    1.774    0.032    0.435
   2_xyz:    1.272    0.046    0.567
   2_adp:    1.272    0.046    0.567
   2_occ:    1.272    0.046    0.567
   3_bss:    1.272    0.046    0.567
   3_xyz:    1.240    0.060    0.653
   3_adp:    1.240    0.060    0.653
   3_occ:    1.240    0.060    0.653
   4_bss:    1.240    0.060    0.653
   4_xyz:    1.391    0.062    0.686
   4_adp:    1.391    0.062    0.686
   4_occ:    1.391    0.062    0.686
   5_bss:    1.391    0.062    0.686
   5_xyz:    1.468    0.093    0.694
   5_adp:    1.468    0.093    0.694
   5_occ:    1.468    0.093    0.694
   5_bss:    1.468    0.093    0.694
------------------------------------------------------------------------

CPU time actual refinement: 344.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/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_618/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_618/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.27 
  Macro-tasks:
    bulk solvent and scale       = 37.47  
    individual site refinement   = 153.80 
    weights calculation          = 28.91  
    collect and process          = 6.39   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 226.66 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 111.33 
    alpha_beta                      = 7.78   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 123.33 
    fmodel                         = 6.53   
    r_factors                      = 0.29   
    phase_errors                   = 10.51  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 262.97 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.721 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    682 calls, 111.04 s
gradients_fft:          627 calls, 108.18 s

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

# Date 2008-01-16 Time 05:15:25 PST -0800 (1200489325.97 s)
Start R-work = 0.4315, R-free = 0.4295 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1743 (no bulk solvent and anisotropic scale)

Start R-work = 0.4188, R-free = 0.4169
Final R-work = 0.1100, R-free = 0.1550