# Date 2008-01-16 Time 05:07:33 PST -0800 (1200488853.42 s)
#phil __OFF__

Command line arguments: "../602.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25639
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 602

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 48.1033, 87.6859, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 1.99075
Completeness in resolution range: 0.940242
Completeness with d_max=infinity: 0.937362

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0589
                             d_min =   1.9908

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 1.99075
Completeness in resolution range: 0.940242
Completeness with d_max=infinity: 0.937362

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0593 -  4.2596 [2194/2222]  1971   223  10.2%
  bin  2:  4.2596 -  3.3937 [2090/2113]  1884   206   9.9%
  bin  3:  3.3937 -  2.9685 [2069/2094]  1862   207  10.0%
  bin  4:  2.9685 -  2.6988 [2068/2084]  1857   211  10.2%
  bin  5:  2.6988 -  2.5063 [2015/2052]  1814   201  10.0%
  bin  6:  2.5063 -  2.3591 [2049/2083]  1850   199   9.7%
  bin  7:  2.3591 -  2.2413 [2015/2052]  1813   202  10.0%
  bin  8:  2.2413 -  2.1441 [2003/2045]  1803   200  10.0%
  bin  9:  2.1441 -  2.0617 [2018/2057]  1822   196   9.7%
  bin 10:  2.0617 -  1.9908 [1068/2032]   954   114  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/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:
        1.81 -     2.42: 25
        2.42 -     3.04: 2154
        3.04 -     3.66: 4605
        3.66 -     4.28: 8858
        4.28 -     4.90: 12208
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.831 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.991 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  2.107 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.120 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27845 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_602/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 48.10325 87.68585 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: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4553   r_free= 0.4427   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.270554                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7509 0.99   1422  158 0.3656 0.3806      6.5457      6.5507|
|  2:  4.7509 -  3.7907 0.99   1368  152 0.4022 0.4160      6.8357      6.8429|
|  3:  3.7907 -  3.3174 0.99   1346  149 0.4382 0.4016      6.6761      6.6111|
|  4:  3.3174 -  3.0168 0.99   1322  144 0.4487 0.4168      6.5059      6.4575|
|  5:  3.0168 -  2.8020 0.98   1327  147 0.4874 0.4229      6.3508        6.36|
|  6:  2.8020 -  2.6377 0.99   1309  148 0.4881 0.4674      6.2707      6.1232|
|  7:  2.6377 -  2.5063 0.99   1294  150 0.4728 0.4273      6.2187      6.1453|
|  8:  2.5063 -  2.3976 0.99   1333  140 0.4866 0.4956       6.157      6.1492|
|  9:  2.3976 -  2.3057 0.99   1299  148 0.4847 0.4628      6.0964      6.1669|
| 10:  2.3057 -  2.2263 0.98   1301  139 0.5021 0.4471      6.0864      6.0308|
| 11:  2.2263 -  2.1569 0.98   1290  147 0.5080 0.5017      6.0236      6.0206|
| 12:  2.1569 -  2.0955 1.00   1285  150 0.4947 0.5301      5.9387      5.9885|
| 13:  2.0955 -  2.0404 0.96   1271  130 0.5050 0.5310       5.871      5.8482|
| 14:  2.0404 -  1.9908 0.36    463   57 0.4685 0.4527      5.8584      5.6798|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0593 -  4.7509  1422   158  0.69  34.72   0.82     0.73      72716.02|
|  2:  4.7509 -  3.7907  1368   152  0.71  34.08   0.90     0.80     100309.58|
|  3:  3.7907 -  3.3174  1346   149  0.63  41.41   0.88     0.79     102950.36|
|  4:  3.3174 -  3.0168  1322   144  0.56  46.95   0.89     0.73      87978.60|
|  5:  3.0168 -  2.8020  1327   147  0.50  52.31   0.88     0.67      68210.99|
|  6:  2.8020 -  2.6377  1309   148  0.48  53.67   0.88     0.64      58019.87|
|  7:  2.6377 -  2.5063  1294   150  0.47  54.41   0.93     0.62      53932.85|
|  8:  2.5063 -  2.3976  1333   140  0.46  55.43   0.90     0.62      49838.73|
|  9:  2.3976 -  2.3057  1299   148  0.45  55.97   0.92     0.64      46751.16|
| 10:  2.3057 -  2.2263  1301   139  0.47  54.93   0.92     0.65      41023.93|
| 11:  2.2263 -  2.1569  1290   147  0.41  59.14   0.92     0.62      42019.99|
| 12:  2.1569 -  2.0955  1285   150  0.35  63.61   0.92     0.53      42269.67|
| 13:  2.0955 -  2.0404  1271   130  0.29  68.17   0.90     0.45      38909.72|
| 14:  2.0404 -  1.9908   463    57  0.34  64.94   1.01     0.43      28337.70|
|alpha:            min =        0.43 max =            0.80 mean =         0.65|
|beta:             min =    28337.70 max =       102950.36 mean =     61451.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.00|
|phase err.(test): min =        0.00 max =           89.91 mean =        52.32|
|-----------------------------------------------------------------------------|

============================== 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 = 10.149659             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.487   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.820165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.057   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      182 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1972 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1833 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2772 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4574 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4284 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5572 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6636 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.209 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    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: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4553   r_free= 0.4427   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.270554                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4450   r_free= 0.4303   ksol= 0.28   Bsol= 32.14   scale= 0.922   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.72,4.90,1.18,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.262532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.827315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.942   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.988648              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.761   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4450      final r-factor (work) = 0.3534          |
| start r-factor (free) = 0.4303      final r-factor (free) = 0.3808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7942 = 8.83 * 0.50 * 6.2596 + 1.00 * 0.1667                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2173 = 8.83 * 0.50 * 6.1400 + 1.00 * 0.1173                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3534      final r-factor (work) = 0.3256          |
| start r-factor (free) = 0.3808      final r-factor (free) = 0.3932          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0762 = 0.99 * 1.00 * 6.1400 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0113 = 0.99 * 1.00 * 6.0593 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.78   18.46    None  None   None       |
|    all(noH): 2823   0      0.00    97.78   18.46    None  None   None       |
|    Sol.    : 438    0      0.00    97.78   36.56    None  None   None       |
|    Mac.    : 2385   0      0.00    77.59   15.14    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 -   9.778:  884   |   5:    48.890 -  58.669:   71        |
|      1:     9.778 -  19.556:  933   |   6:    58.669 -  68.447:   35        |
|      2:    19.556 -  29.334:  481   |   7:    68.447 -  78.225:   22        |
|      3:    29.334 -  39.112:  252   |   8:    78.225 -  88.003:    5        |
|      4:    39.112 -  48.890:  138   |   9:    88.003 -  97.781:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3256 r_free = 0.3932             target_work(ml) = 6.064         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3252 r_free = 0.3930             target_work(ml) = 6.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3252   r_free= 0.3930   ksol= 0.28   Bsol= 32.14   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.72,4.90,1.18,0.00,0.00,0.00); trace/3= 0.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.062892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3245   r_free= 0.3905   ksol= 0.27   Bsol= 48.43   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,2.88,0.81,0.00,0.00,0.00); trace/3= 0.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.064723                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.349071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.399   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.518503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.611  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3245      final r-factor (work) = 0.2656          |
| start r-factor (free) = 0.3905      final r-factor (free) = 0.3236          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.4205 = 8.35 * 0.50 * 6.0613 + 1.00 * 0.1173                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.0809 = 8.35 * 0.50 * 5.9849 + 1.00 * 0.0967                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2656      final r-factor (work) = 0.2517          |
| start r-factor (free) = 0.3236      final r-factor (free) = 0.3134          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1223 = 0.52 * 1.00 * 5.9849 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0615 = 0.52 * 1.00 * 5.8734 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.15   17.76    None  None   None       |
|    all(noH): 2823   0      0.00    96.15   17.76    None  None   None       |
|    Sol.    : 438    0      0.00    96.15   36.93    None  None   None       |
|    Mac.    : 2385   0      0.00    94.01   14.24    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 -   9.615:  933   |   5:    48.074 -  57.688:   91        |
|      1:     9.615 -  19.229:  983   |   6:    57.688 -  67.303:   38        |
|      2:    19.229 -  28.844:  416   |   7:    67.303 -  76.918:   21        |
|      3:    28.844 -  38.459:  222   |   8:    76.918 -  86.532:    6        |
|      4:    38.459 -  48.074:  109   |   9:    86.532 -  96.147:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2517 r_free = 0.3134             target_work(ml) = 5.864         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2516 r_free = 0.3132             target_work(ml) = 5.863         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2516   r_free= 0.3132   ksol= 0.27   Bsol= 48.43   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,2.88,0.81,0.00,0.00,0.00); trace/3= 0.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.863280                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2515   r_free= 0.3128   ksol= 0.32   Bsol= 61.79   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,1.58,0.38,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.863750                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.749369              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.837   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.498225              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.677  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.2097          |
| start r-factor (free) = 0.3128      final r-factor (free) = 0.2600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1071 = 3.75 * 0.50 * 5.8732 + 1.00 * 0.0967                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9094 = 3.75 * 0.50 * 5.7857 + 1.00 * 0.0630                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2097      final r-factor (work) = 0.1959          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.2470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8995 = 0.50 * 1.00 * 5.7857 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8368 = 0.50 * 1.00 * 5.6566 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.00   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    95.00   17.71    None  None   None       |
|    Sol.    : 438    0      3.35    95.00   41.39    None  None   None       |
|    Mac.    : 2385   0      0.00    88.83   13.37    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 -   9.500: 1048   |   5:    47.501 -  57.002:  103        |
|      1:     9.500 -  19.001:  994   |   6:    57.002 -  66.502:   57        |
|      2:    19.001 -  28.501:  274   |   7:    66.502 -  76.002:   30        |
|      3:    28.501 -  38.001:  169   |   8:    76.002 -  85.502:   16        |
|      4:    38.001 -  47.501:  125   |   9:    85.502 -  95.003:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1959 r_free = 0.2470             target_work(ml) = 5.636         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1958 r_free = 0.2471             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.2471   ksol= 0.32   Bsol= 61.79   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,1.58,0.38,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.635376                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.2470   ksol= 0.33   Bsol= 76.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,0.41,-0.06,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.636355                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.194241              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.348  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.442991              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.299   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1958      final r-factor (work) = 0.1497          |
| start r-factor (free) = 0.2470      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7578 = 5.19 * 0.50 * 5.6581 + 1.00 * 0.0630                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4289 = 5.19 * 0.50 * 5.5236 + 1.00 * 0.0834                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1497      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1855          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4640 = 0.44 * 1.00 * 5.5236 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3815 = 0.44 * 1.00 * 5.3492 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.27   17.31    None  None   None       |
|    all(noH): 2823   0      0.00    95.27   17.31    None  None   None       |
|    Sol.    : 438    0      0.00    95.27   42.76    None  None   None       |
|    Mac.    : 2385   0      0.35    91.56   12.64    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 -   9.527: 1086   |   5:    47.635 -  57.162:   95        |
|      1:     9.527 -  19.054: 1046   |   6:    57.162 -  66.689:   67        |
|      2:    19.054 -  28.581:  231   |   7:    66.689 -  76.216:   41        |
|      3:    28.581 -  38.108:  125   |   8:    76.216 -  85.743:   14        |
|      4:    38.108 -  47.635:  110   |   9:    85.743 -  95.271:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1380 r_free = 0.1855             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1379 r_free = 0.1854             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1854   ksol= 0.33   Bsol= 76.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,0.41,-0.06,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.319193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1851   ksol= 0.33   Bsol= 75.14   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.33,0.02,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.319438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.706018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.874  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.383403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.124  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1851      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3221 = 2.71 * 0.50 * 5.3501 + 1.00 * 0.0834                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2182 = 2.71 * 0.50 * 5.2850 + 1.00 * 0.0676                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3229 = 1.38 * 1.00 * 5.2850 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2681 = 1.38 * 1.00 * 5.2442 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.46  17.36    None  None   None       |
|    all(noH): 2823   0      0.00    107.46  17.36    None  None   None       |
|    Sol.    : 438    0      0.00    106.25  44.51    None  None   None       |
|    Mac.    : 2385   0      0.00    107.46  12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.746: 1360   |   5:    53.730 -  64.476:   81        |
|      1:    10.746 -  21.492:  881   |   6:    64.476 -  75.222:   53        |
|      2:    21.492 -  32.238:  184   |   7:    75.222 -  85.969:   30        |
|      3:    32.238 -  42.984:  119   |   8:    85.969 -  96.715:   12        |
|      4:    42.984 -  53.730:   98   |   9:    96.715 - 107.461:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1727             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1727             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1727   ksol= 0.33   Bsol= 75.14   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.33,0.02,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238915                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7509 0.99   1422  158 0.0994 0.1362      5.4111       5.605|
|  2:  4.7509 -  3.7907 0.99   1368  152 0.0861 0.1050      5.4502      5.6231|
|  3:  3.7907 -  3.3174 0.99   1346  149 0.1125 0.1641       5.528      5.9073|
|  4:  3.3174 -  3.0168 0.99   1322  144 0.1353 0.1772      5.5312      5.6817|
|  5:  3.0168 -  2.8020 0.98   1327  147 0.1501 0.1820      5.4349       5.587|
|  6:  2.8020 -  2.6377 0.99   1309  148 0.1438 0.2312      5.3343       5.585|
|  7:  2.6377 -  2.5063 0.99   1294  150 0.1425 0.1810      5.2783      5.4639|
|  8:  2.5063 -  2.3976 0.99   1333  140 0.1334 0.1943       5.203      5.4243|
|  9:  2.3976 -  2.3057 0.99   1299  148 0.1353 0.2128      5.1396      5.4721|
| 10:  2.3057 -  2.2263 0.98   1301  139 0.1309 0.1712      5.0769      5.2195|
| 11:  2.2263 -  2.1569 0.98   1290  147 0.1289 0.2077      5.0143      5.3514|
| 12:  2.1569 -  2.0955 1.00   1285  150 0.1237 0.1717      4.9395      5.1966|
| 13:  2.0955 -  2.0404 0.96   1271  130 0.1288 0.1870      4.8679      5.0774|
| 14:  2.0404 -  1.9908 0.36    463   57 0.1124 0.2080       4.782      5.0361|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0593 -  4.7509  1422   158  0.94   9.64   0.96     0.93       7633.18|
|  2:  4.7509 -  3.7907  1368   152  0.95   8.46   1.00     0.99       9571.59|
|  3:  3.7907 -  3.3174  1346   149  0.93  12.07   1.02     1.02      11414.33|
|  4:  3.3174 -  3.0168  1322   144  0.91  15.23   1.01     1.00      11950.94|
|  5:  3.0168 -  2.8020  1327   147  0.88  18.01   1.00     0.99      10376.04|
|  6:  2.8020 -  2.6377  1309   148  0.88  18.62   0.98     0.94       8943.85|
|  7:  2.6377 -  2.5063  1294   150  0.89  17.69   0.99     0.97       7822.40|
|  8:  2.5063 -  2.3976  1333   140  0.88  18.05   0.99     0.95       7164.49|
|  9:  2.3976 -  2.3057  1299   148  0.88  18.19   0.99     0.93       6102.65|
| 10:  2.3057 -  2.2263  1301   139  0.88  18.28   0.98     0.94       5639.77|
| 11:  2.2263 -  2.1569  1290   147  0.89  17.86   0.98     0.94       5052.34|
| 12:  2.1569 -  2.0955  1285   150  0.90  17.03   0.99     0.98       4513.04|
| 13:  2.0955 -  2.0404  1271   130  0.88  18.16   0.97     0.96       3914.64|
| 14:  2.0404 -  1.9908   463    57  0.89  16.77   0.95     0.90       3265.23|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3265.23 max =        11950.94 mean =      7619.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.89|
|phase err.(test): min =        0.00 max =           89.03 mean =        15.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1726   ksol= 0.33   Bsol= 74.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.34,0.25,-0.00,0.00,0.00); trace/3= -0.59                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1726   ksol= 0.33   Bsol= 74.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.34,0.25,-0.00,0.00,0.00); trace/3= -0.59                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238775                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7509 0.99   1422  158 0.0992 0.1356       5.409      5.6046|
|  2:  4.7509 -  3.7907 0.99   1368  152 0.0861 0.1051      5.4504      5.6236|
|  3:  3.7907 -  3.3174 0.99   1346  149 0.1126 0.1642      5.5285      5.9078|
|  4:  3.3174 -  3.0168 0.99   1322  144 0.1353 0.1772      5.5312      5.6816|
|  5:  3.0168 -  2.8020 0.98   1327  147 0.1502 0.1821      5.4348      5.5862|
|  6:  2.8020 -  2.6377 0.99   1309  148 0.1436 0.2308      5.3334      5.5837|
|  7:  2.6377 -  2.5063 0.99   1294  150 0.1425 0.1812      5.2782      5.4637|
|  8:  2.5063 -  2.3976 0.99   1333  140 0.1333 0.1943      5.2032      5.4247|
|  9:  2.3976 -  2.3057 0.99   1299  148 0.1353 0.2128        5.14      5.4727|
| 10:  2.3057 -  2.2263 0.98   1301  139 0.1307 0.1716      5.0773      5.2205|
| 11:  2.2263 -  2.1569 0.98   1290  147 0.1288 0.2078      5.0141      5.3513|
| 12:  2.1569 -  2.0955 1.00   1285  150 0.1238 0.1721      4.9395      5.1976|
| 13:  2.0955 -  2.0404 0.96   1271  130 0.1290 0.1862      4.8679       5.075|
| 14:  2.0404 -  1.9908 0.36    463   57 0.1123 0.2081      4.7822      5.0369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0593 -  4.7509  1422   158  0.94   9.61   0.96     0.93       7589.40|
|  2:  4.7509 -  3.7907  1368   152  0.95   8.46   1.01     0.99       9561.29|
|  3:  3.7907 -  3.3174  1346   149  0.93  12.09   1.03     1.02      11434.46|
|  4:  3.3174 -  3.0168  1322   144  0.91  15.24   1.01     1.00      11952.75|
|  5:  3.0168 -  2.8020  1327   147  0.88  18.00   1.01     0.99      10360.09|
|  6:  2.8020 -  2.6377  1309   148  0.88  18.60   0.99     0.95       8927.02|
|  7:  2.6377 -  2.5063  1294   150  0.89  17.68   1.00     0.97       7815.25|
|  8:  2.5063 -  2.3976  1333   140  0.88  18.06   0.99     0.95       7168.71|
|  9:  2.3976 -  2.3057  1299   148  0.88  18.21   1.00     0.94       6110.51|
| 10:  2.3057 -  2.2263  1301   139  0.88  18.29   0.99     0.95       5646.15|
| 11:  2.2263 -  2.1569  1290   147  0.89  17.86   0.99     0.95       5056.23|
| 12:  2.1569 -  2.0955  1285   150  0.90  17.03   1.00     0.99       4513.75|
| 13:  2.0955 -  2.0404  1271   130  0.88  18.15   0.98     0.96       3908.73|
| 14:  2.0404 -  1.9908   463    57  0.89  16.76   0.96     0.91       3257.95|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3257.95 max =        11952.75 mean =      7614.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.88|
|phase err.(test): min =        0.00 max =           89.03 mean =        15.30|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.46  17.37    None  None   None       |
|    all(noH): 2823   0      0.00    107.46  17.37    None  None   None       |
|    Sol.    : 438    0      0.00    106.25  44.52    None  None   None       |
|    Mac.    : 2385   0      0.00    107.46  12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.749: 1360   |   5:    53.733 -  64.479:   81        |
|      1:    10.749 -  21.495:  881   |   6:    64.479 -  75.225:   53        |
|      2:    21.495 -  32.241:  184   |   7:    75.225 -  85.971:   30        |
|      3:    32.241 -  42.987:  119   |   8:    85.971 -  96.718:   12        |
|      4:    42.987 -  53.733:   98   |   9:    96.718 - 107.464:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.490 - 5.602
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 338
   mapped sites are within: 0.743 - 5.602

peak=    5.865 closest distance to " O   HOH Z 210 " =    1.422
peak=    5.425 closest distance to " O   GLN A  11 " =    1.045
peak=    5.100 closest distance to " O   HOH Z  49 " =    1.335
peak=    5.013 closest distance to " O   HOH Z 113 " =    2.036
peak=    4.963 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.931 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.884 closest distance to " CG  PRO A  54 " =    1.364
peak=    4.776 closest distance to " O   PRO A 198 " =    1.533
peak=    4.730 closest distance to " CB  SER A  63 " =    1.197
peak=    4.658 closest distance to " O   HOH Z 433 " =    1.813
peak=    4.589 closest distance to " O   HOH Z 403 " =    1.949
peak=    4.544 closest distance to " CG  PRO A  90 " =    1.275
peak=    4.538 closest distance to " O   HOH Z  43 " =    2.282
peak=    4.498 closest distance to " CA  ALA A  51 " =    1.035
peak=    4.483 closest distance to " CB  ARG A 190 " =    1.854
peak=    4.482 closest distance to " O   HOH Z 134 " =    1.917
peak=    4.404 closest distance to " CB  GLN A 183 " =    1.285
peak=    4.384 closest distance to " CB  ARG A 275 " =    0.837
peak=    4.382 closest distance to " CG  PRO A 198 " =    1.144
peak=    4.352 closest distance to " NH2 ARG A 156 " =    1.194
peak=    4.338 closest distance to " O   HOH Z 412 " =    3.428
peak=    4.301 closest distance to " O   HOH Z 130 " =    2.680
peak=    4.294 closest distance to " CD2 TRP A 179 " =    1.324
peak=    4.252 closest distance to " NE2 GLN A  11 " =    1.119
peak=    4.194 closest distance to " O   HOH Z 209 " =    2.269
peak=    4.154 closest distance to " O   HOH Z 248 " =    1.521
peak=    4.143 closest distance to " O   ALA A 165 " =    1.377
peak=    4.139 closest distance to " CZ  PHE A 218 " =    1.173
peak=    4.125 closest distance to " CZ  PHE A  38 " =    1.198
peak=    4.122 closest distance to " O   HOH Z 234 " =    3.783
peak=    4.114 closest distance to " O   HOH Z 232 " =    2.500
peak=    4.110 closest distance to " O   HOH Z 214 " =    1.578
peak=    4.087 closest distance to " CB  GLU A 128 " =    1.148
peak=    4.078 closest distance to " O   HOH Z 431 " =    1.184
peak=    4.071 closest distance to " O   HOH Z  44 " =    1.944
peak=    4.057 closest distance to " O   HOH Z 298 " =    1.960
peak=    4.041 closest distance to " CA  ARG A 195 " =    1.131
peak=    4.041 closest distance to " O   HOH Z 357 " =    2.223
peak=    4.028 closest distance to " O   HOH Z 261 " =    2.384
peak=    4.011 closest distance to " CB  TRP A 179 " =    1.275
peak=    4.005 closest distance to " CB  ASN A 148 " =    1.449
peak=    3.993 closest distance to " CB  PRO A  54 " =    0.932
peak=    3.984 closest distance to " O   ASP A 124 " =    1.623
peak=    3.983 closest distance to " CD  LYS A 166 " =    1.478
peak=    3.978 closest distance to " CG  PRO A 213 " =    1.231
peak=    3.974 closest distance to " O   HOH Z 132 " =    2.631
peak=    3.965 closest distance to " O   HOH Z  65 " =    1.009
peak=    3.958 closest distance to " CG  GLN A  11 " =    1.327
peak=    3.950 closest distance to " O   HOH Z 196 " =    1.485
peak=    3.947 closest distance to " O   HOH Z 336 " =    1.854
peak=    3.946 closest distance to " CZ3 TRP A 266 " =    1.095
peak=    3.945 closest distance to " O   HOH Z  80 " =    1.954
peak=    3.931 closest distance to " CA  ALA A 160 " =    0.944
peak=    3.917 closest distance to " CA  ARG A  36 " =    1.048
peak=    3.909 closest distance to " O   HOH Z 189 " =    2.832
peak=    3.905 closest distance to " O   HOH Z 437 " =    1.771
peak=    3.902 closest distance to " O   HOH Z  63 " =    2.117
peak=    3.902 closest distance to " O   HOH Z 406 " =    1.636
peak=    3.901 closest distance to " CB  GLU A 277 " =    3.808
peak=    3.901 closest distance to " O   HOH Z 369 " =    2.067
peak=    3.885 closest distance to " O   HOH Z 402 " =    1.731
peak=    3.883 closest distance to " O   HOH Z 117 " =    1.140
peak=    3.868 closest distance to " CG2 VAL A 197 " =    1.209
peak=    3.843 closest distance to " O   HOH Z 176 " =    1.675
peak=    3.838 closest distance to " O   HOH Z 102 " =    1.394
peak=    3.835 closest distance to " O   HOH Z 346 " =    1.554
peak=    3.834 closest distance to " O   ASN A  74 " =    1.734
peak=    3.831 closest distance to " CG1 ILE A  33 " =    1.200
peak=    3.830 closest distance to " O   SER A  87 " =    2.286
peak=    3.823 closest distance to " O   HOH Z 258 " =    2.196
peak=    3.823 closest distance to " O   HOH Z 132 " =    2.918
peak=    3.822 closest distance to " O   HOH Z 417 " =    2.852
peak=    3.820 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.782 closest distance to " CG2BVAL A  41 " =    0.907
peak=    3.777 closest distance to " O   HOH Z 265 " =    1.961
peak=    3.769 closest distance to " CB  VAL A 202 " =    1.553
peak=    3.767 closest distance to " CB  THR A  52 " =    0.860
peak=    3.760 closest distance to " N   SER A 164 " =    0.976
peak=    3.755 closest distance to " O   HOH Z 403 " =    1.441
peak=    3.755 closest distance to " O   HOH Z 394 " =    1.595
peak=    3.752 closest distance to " O   HOH Z 214 " =    2.766
peak=    3.749 closest distance to " O   HOH Z 361 " =    3.323
peak=    3.743 closest distance to " CB  GLU A 152 " =    1.108
peak=    3.737 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.722 closest distance to " CA  LEU A  83 " =    1.283
peak=    3.716 closest distance to " CD  ARG A 159 " =    0.870
peak=    3.709 closest distance to " O   HOH Z  40 " =    2.001
peak=    3.709 closest distance to " O   HOH Z 154 " =    1.564
peak=    3.706 closest distance to " CB  SER A  62 " =    0.811
peak=    3.705 closest distance to " O   HOH Z 246 " =    1.537
peak=    3.700 closest distance to " O   HOH Z 418 " =    1.826
peak=    3.695 closest distance to " O   HOH Z 203 " =    1.762
peak=    3.693 closest distance to " CA  TYR A 116 " =    1.433
peak=    3.686 closest distance to " O   HOH Z 128 " =    2.057
peak=    3.683 closest distance to " O   HOH Z 126 " =    1.622
peak=    3.681 closest distance to " OG BSER A 164 " =    2.266
peak=    3.679 closest distance to " CA  ASN A 215 " =    1.110
peak=    3.678 closest distance to " O   HOH Z  78 " =    1.824
peak=    3.676 closest distance to " CB  SER A 141 " =    1.086
peak=    3.670 closest distance to " O   HOH Z  35 " =    1.980
peak=    3.669 closest distance to " CA  SER A  12 " =    1.490
peak=    3.668 closest distance to " CG AARG A 275 " =    1.158
peak=    3.667 closest distance to " OD1 ASN A 301 " =    1.089
peak=    3.666 closest distance to " CA  ASN A 217 " =    1.313
peak=    3.654 closest distance to " CA  GLU A 152 " =    0.906
peak=    3.653 closest distance to " N   CYS A 260 " =    0.916
peak=    3.653 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.653 closest distance to " CD  ARG A 269 " =    1.006
peak=    3.652 closest distance to " O   HOH Z  20 " =    1.681
peak=    3.651 closest distance to " O   HOH Z 139 " =    1.255
peak=    3.648 closest distance to " CB  MET A 105 " =    1.155
peak=    3.645 closest distance to " O   HOH Z 339 " =    1.316
peak=    3.643 closest distance to " O   HOH Z 128 " =    1.420
peak=    3.641 closest distance to " O  BHOH Z 338 " =    1.069
peak=    3.637 closest distance to " CB  ASN A 285 " =    0.900
peak=    3.636 closest distance to " CB  ARG A  79 " =    1.368
peak=    3.635 closest distance to " NE2 GLN A  77 " =    3.187
peak=    3.633 closest distance to " O   HOH Z 422 " =    0.782
peak=    3.632 closest distance to " CG2 ILE A  20 " =    1.407
peak=    3.629 closest distance to " CB  GLU A  46 " =    1.059
peak=    3.626 closest distance to " O   TYR A 116 " =    1.449
peak=    3.625 closest distance to " CD1 LEU A  96 " =    0.743
peak=    3.623 closest distance to " O   HOH Z 423 " =    1.789
peak=    3.615 closest distance to " CB  TRP A 266 " =    1.029
peak=    3.603 closest distance to " O   HOH Z  15 " =    2.104
peak=    3.600 closest distance to " O   HOH Z 154 " =    2.331
peak=    3.592 closest distance to " CD  ARG A 195 " =    0.981
peak=    3.591 closest distance to " CA  ASN A 176 " =    1.610
peak=    3.573 closest distance to " O  BHOH Z 338 " =    2.128
peak=    3.573 closest distance to " O   HOH Z 146 " =    1.642
peak=    3.573 closest distance to " O   GLY A  91 " =    1.192
peak=    3.571 closest distance to " O   HOH Z 368 " =    2.122
peak=    3.565 closest distance to " CA  VAL A 125 " =    1.324
peak=    3.563 closest distance to " O   HOH Z 147 " =    1.701
peak=    3.562 closest distance to " O   HOH Z 316 " =    3.059
peak=    3.560 closest distance to " CG  ARG A 219 " =    1.217
peak=    3.559 closest distance to " CB  ASN A 142 " =    1.177
peak=    3.551 closest distance to " O   HOH Z 389 " =    2.150
peak=    3.550 closest distance to " O   HOH Z 394 " =    3.973
peak=    3.542 closest distance to " CA  ALA A 295 " =    1.096
peak=    3.542 closest distance to " O   THR A 251 " =    1.345
peak=    3.537 closest distance to " CB  ARG A  79 " =    0.913
peak=    3.534 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.531 closest distance to " N   HIS A 108 " =    1.804
peak=    3.530 closest distance to " CA  GLY A 196 " =    1.004
peak=    3.529 closest distance to " CA  ALA A  21 " =    1.436
peak=    3.528 closest distance to " CA  THR A 246 " =    1.043
peak=    3.520 closest distance to " O   HOH Z 299 " =    4.172
peak=    3.518 closest distance to " NE2 HIS A 115 " =    1.106
peak=    3.517 closest distance to " O   HOH Z 427 " =    3.147
peak=    3.514 closest distance to " O   HOH Z 156 " =    2.584
peak=    3.512 closest distance to " N   TYR A 116 " =    1.595
peak=    3.510 closest distance to " CB  PHE A  16 " =    1.180
peak=    3.506 closest distance to " O   HOH Z   7 " =    1.048
peak=    3.501 closest distance to " CB  PRO A  54 " =    1.337
peak=    3.493 closest distance to " CA  THR A  82 " =    1.512
peak=    3.489 closest distance to " O   HOH Z 383 " =    2.164
peak=    3.489 closest distance to " CA  ALA A 100 " =    1.207
peak=    3.488 closest distance to " CB  PRO A 243 " =    1.353
peak=    3.475 closest distance to " O   HOH Z  54 " =    1.083
peak=    3.472 closest distance to " CZ3 TRP A  85 " =    0.885
peak=    3.469 closest distance to " O   ASP A 200 " =    1.623
peak=    3.468 closest distance to " O   PHE A  61 " =    1.449
peak=    3.466 closest distance to " O   HOH Z  48 " =    1.902
peak=    3.463 closest distance to " O   HOH Z  88 " =    3.242
peak=    3.463 closest distance to " O   HOH Z 185 " =    1.716
peak=    3.453 closest distance to " CD  PRO A  54 " =    1.025
peak=    3.451 closest distance to " O   HOH Z  47 " =    2.552
peak=    3.448 closest distance to " CD1 LEU A 300 " =    1.153
peak=    3.445 closest distance to " CA  ILE A 106 " =    0.824
peak=    3.444 closest distance to " CD  GLN A 194 " =    1.644
peak=    3.434 closest distance to " CB  SER A   3 " =    1.412
peak=    3.434 closest distance to " O   HOH Z 425 " =    1.475
peak=    3.433 closest distance to " CB  VAL A 265 " =    1.211
peak=    3.433 closest distance to " O   HOH Z 374 " =    2.733
peak=    3.429 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.425 closest distance to " NZ  LYS A 117 " =    3.052
peak=    3.423 closest distance to " O   HOH Z 284 " =    2.906
peak=    3.421 closest distance to " O   HOH Z 142 " =    1.416
peak=    3.416 closest distance to " N   ASN A  39 " =    1.300
peak=    3.415 closest distance to " CA  LYS A 166 " =    1.351
peak=    3.415 closest distance to " O   HOH Z 313 " =    1.875
peak=    3.413 closest distance to " CG  GLN A  58 " =    0.923
peak=    3.411 closest distance to " CB  GLU A  37 " =    0.825
peak=    3.410 closest distance to " OE1 GLN A  11 " =    2.192
peak=    3.409 closest distance to " O   HOH Z 414 " =    1.781
peak=    3.408 closest distance to " OH  TYR A 116 " =    1.287
peak=    3.405 closest distance to " CA  THR A 221 " =    1.708
peak=    3.398 closest distance to " O   HOH Z  90 " =    3.645
peak=    3.395 closest distance to " CB  ARG A 269 " =    0.800
peak=    3.395 closest distance to " O   HOH Z 251 " =    1.504
peak=    3.394 closest distance to " CE  LYS A  76 " =    0.839
peak=    3.391 closest distance to " NH1AARG A 145 " =    1.273
peak=    3.389 closest distance to " CG1BVAL A  72 " =    1.862
peak=    3.388 closest distance to " O   HOH Z 358 " =    1.312
peak=    3.383 closest distance to " CA  ASP A 162 " =    1.179
peak=    3.382 closest distance to " CD2 LEU A 297 " =    0.801
peak=    3.380 closest distance to " N   ILE A  33 " =    0.984
peak=    3.378 closest distance to " O   HOH Z 421 " =    2.108
peak=    3.374 closest distance to " O   HOH Z 146 " =    1.262
peak=    3.373 closest distance to " CG  PRO A 243 " =    1.124
peak=    3.367 closest distance to " OE1 GLN A  58 " =    3.441
peak=    3.365 closest distance to " C   GLY A  80 " =    1.071
peak=    3.359 closest distance to " OD1 ASN A  69 " =    2.379
peak=    3.358 closest distance to " CA  SER A  32 " =    1.649
peak=    3.353 closest distance to " CB  ALA A 248 " =    1.284
peak=    3.353 closest distance to " N   ASN A 252 " =    1.217
peak=    3.352 closest distance to " CG2 THR A 220 " =    0.850
peak=    3.350 closest distance to " O   HOH Z 404 " =    1.628
peak=    3.349 closest distance to " CG2 THR A 221 " =    1.218
peak=    3.343 closest distance to " O   HOH Z  30 " =    1.305
peak=    3.338 closest distance to " CG  GLU A  37 " =    0.991
peak=    3.338 closest distance to " O   HOH Z 240 " =    2.513
peak=    3.338 closest distance to " O   HOH Z 126 " =    2.356
peak=    3.337 closest distance to " O   HOH Z 285 " =    2.870
peak=    3.335 closest distance to " O   HOH Z 124 " =    1.063
peak=    3.332 closest distance to " O   HOH Z 216 " =    5.391
peak=    3.330 closest distance to " CG2 THR A  29 " =    1.383
peak=    3.329 closest distance to " OG  SER A 245 " =    1.585
peak=    3.328 closest distance to " O   HOH Z 345 " =    1.674
peak=    3.324 closest distance to " OG  SER A  62 " =    2.819
peak=    3.319 closest distance to " O   HOH Z 428 " =    1.045
peak=    3.316 closest distance to " O   HOH Z 117 " =    2.062
peak=    3.314 closest distance to " N   GLU A  44 " =    1.380
peak=    3.314 closest distance to " CG1 VAL A 153 " =    1.091
peak=    3.311 closest distance to " NH2BARG A 145 " =    2.032
peak=    3.311 closest distance to " O   HOH Z 271 " =    2.627
peak=    3.309 closest distance to " O   HOH Z 377 " =    1.146
peak=    3.304 closest distance to " CB  LEU A 228 " =    1.174
peak=    3.304 closest distance to " O   HOH Z 207 " =    1.567
peak=    3.302 closest distance to " O   PRO A 213 " =    1.518
peak=    3.298 closest distance to " CA  GLU A  46 " =    1.137
peak=    3.297 closest distance to " O   HOH Z 301 " =    1.513
peak=    3.295 closest distance to " O   HOH Z 343 " =    2.249
peak=    3.293 closest distance to " CB  SER A  28 " =    1.066
peak=    3.288 closest distance to " O   HOH Z 298 " =    2.300
peak=    3.287 closest distance to " O   HOH Z 435 " =    2.783
peak=    3.286 closest distance to " O   THR A 220 " =    1.117
peak=    3.284 closest distance to " O   HOH Z 365 " =    2.654
peak=    3.282 closest distance to " O   HOH Z 173 " =    2.285
peak=    3.282 closest distance to " CB  LEU A   5 " =    1.132
peak=    3.281 closest distance to " OG1 THR A 221 " =    1.616
peak=    3.281 closest distance to " O   HOH Z 139 " =    4.827
peak=    3.279 closest distance to " CD  LYS A 119 " =    1.806
peak=    3.277 closest distance to " CB  PRO A  90 " =    1.176
peak=    3.276 closest distance to " CA  ARG A 156 " =    0.969
peak=    3.275 closest distance to " O   HOH Z 141 " =    1.767
peak=    3.262 closest distance to " CA  CYS A 260 " =    1.645
peak=    3.261 closest distance to " O   HOH Z  21 " =    1.854
peak=    3.260 closest distance to " O   HOH Z 109 " =    2.067
peak=    3.259 closest distance to " CB  MET A  40 " =    0.921
peak=    3.259 closest distance to " ND2 ASN A 187 " =    1.525
peak=    3.258 closest distance to " CB  ALA A  71 " =    1.329
peak=    3.256 closest distance to " O   ALA A 158 " =    1.221
peak=    3.251 closest distance to " O   HOH Z 193 " =    2.200
peak=    3.247 closest distance to " O   HOH Z 291 " =    1.404
peak=    3.246 closest distance to " CA  ASP A 191 " =    0.944
peak=    3.242 closest distance to " O   HOH Z 245 " =    1.252
peak=    3.239 closest distance to " O   HOH Z 371 " =    2.771
peak=    3.238 closest distance to " CE1 HIS A 108 " =    1.087
peak=    3.237 closest distance to " O   HOH Z 285 " =    1.654
peak=    3.228 closest distance to " CB  PRO A 198 " =    1.131
peak=    3.228 closest distance to " CG2AVAL A 121 " =    2.021
peak=    3.225 closest distance to " O   HOH Z 193 " =    1.811
peak=    3.223 closest distance to " CD1 ILE A 199 " =    1.145
peak=    3.223 closest distance to " CB  LEU A  83 " =    0.849
peak=    3.222 closest distance to " CB  GLU A 175 " =    1.395
peak=    3.221 closest distance to " O   HOH Z 279 " =    2.134
peak=    3.220 closest distance to " O   HOH Z 435 " =    1.746
peak=    3.220 closest distance to " CA  ASP A 191 " =    1.200
peak=    3.219 closest distance to " O   HOH Z 327 " =    1.766
peak=    3.215 closest distance to " O   HOH Z 423 " =    3.401
peak=    3.214 closest distance to " CB  PHE A 283 " =    0.821
peak=    3.213 closest distance to " CD2 LEU A 255 " =    1.634
peak=    3.210 closest distance to " O   ASP A 191 " =    1.537
peak=    3.208 closest distance to " CE3 TRP A  85 " =    1.172
peak=    3.207 closest distance to " CB  SER A  97 " =    1.302
peak=    3.205 closest distance to " CB  ALA A   9 " =    1.656
peak=    3.202 closest distance to " O   HOH Z  88 " =    1.708
peak=    3.202 closest distance to " O   HOH Z  40 " =    2.317
peak=    3.198 closest distance to " O   HOH Z 294 " =    1.543
peak=    3.194 closest distance to " O   HOH Z 367 " =    1.356
peak=    3.193 closest distance to " N   THR A  52 " =    1.196
peak=    3.193 closest distance to " O   HOH Z  85 " =    2.604
peak=    3.193 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.187 closest distance to " O  BHOH Z  74 " =    1.295
peak=    3.183 closest distance to " CG  GLN A  77 " =    0.921
peak=    3.183 closest distance to " CB  SER A  97 " =    0.875
peak=    3.179 closest distance to " O   HOH Z 189 " =    2.642
peak=    3.179 closest distance to " CB  SER A  26 " =    1.732
peak=    3.176 closest distance to " O   HOH Z  39 " =    1.201
peak=    3.175 closest distance to " O   THR A 251 " =    1.898
peak=    3.173 closest distance to " CB  SER A 210 " =    0.943
peak=    3.173 closest distance to " CB  ASP A 140 " =    0.958
peak=    3.173 closest distance to " O   HOH Z 420 " =    1.930
peak=    3.171 closest distance to " O   HOH Z 244 " =    1.654
peak=    3.171 closest distance to " CA  ASN A 249 " =    1.333
peak=    3.170 closest distance to " CD2 TYR A 186 " =    1.029
peak=    3.168 closest distance to " CG2 VAL A 126 " =    0.854
peak=    3.165 closest distance to " OG  SER A  22 " =    2.700
peak=    3.162 closest distance to " CG  LYS A  76 " =    1.123
peak=    3.160 closest distance to " OG BSER A 258 " =    2.950
peak=    3.160 closest distance to " NH1 ARG A 269 " =    0.749
peak=    3.159 closest distance to " CA  LEU A 101 " =    1.668
peak=    3.158 closest distance to " CA  SER A  87 " =    1.055
peak=    3.156 closest distance to " O   HOH Z 395 " =    1.532
peak=    3.151 closest distance to " CA  ARG A 139 " =    1.382
peak=    3.150 closest distance to " CA  GLN A  73 " =    1.211
peak=    3.147 closest distance to " O   HOH Z 234 " =    1.904
peak=    3.145 closest distance to " O   HOH Z 227 " =    1.731
peak=    3.141 closest distance to " CA  MET A 188 " =    1.012
peak=    3.120 closest distance to " CA  ALA A 291 " =    0.804
peak=    3.116 closest distance to " OD2 ASP A 298 " =    3.710
peak=    3.114 closest distance to " CA  LYS A 117 " =    1.326
peak=    3.113 closest distance to " CG2 ILE A 120 " =    1.222
peak=    3.105 closest distance to " CA  PRO A  90 " =    0.912
peak=    3.103 closest distance to " NZ  LYS A  48 " =    1.225
peak=    3.100 closest distance to " O   HOH Z 430 " =    5.602
peak=    3.099 closest distance to " O   HOH Z 250 " =    1.432
peak=    3.093 closest distance to " O   HOH Z 426 " =    1.265
peak=    3.093 closest distance to " CB  TRP A 179 " =    1.914
peak=    3.091 closest distance to " N   ALA A  10 " =    1.683
peak=    3.082 closest distance to " O   HOH Z 150 " =    1.808
peak=    3.074 closest distance to " O   HOH Z  28 " =    2.229
peak=    3.064 closest distance to " CG1 ILE A 120 " =    1.042
peak=    3.058 closest distance to " O   HOH Z 420 " =    5.118
peak=    3.050 closest distance to " CG2 ILE A 234 " =    1.086
peak=    3.049 closest distance to " CB  ALA A 100 " =    1.333
peak=    3.049 closest distance to " O   HOH Z 116 " =    2.889
peak=    3.046 closest distance to " N   ARG A 156 " =    1.604
peak=    3.042 closest distance to " CG  LEU A 237 " =    1.231
peak=    3.040 closest distance to " ND1 HIS A  81 " =    1.440
peak=    3.036 closest distance to " O   HOH Z   6 " =    1.203
peak=    3.025 closest distance to " O   HOH Z  88 " =    2.304
peak=    3.020 closest distance to " CG1BVAL A  72 " =    3.004
peak=    3.012 closest distance to " NH1 ARG A  14 " =    1.222

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.633 - 5.818
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 218
   mapped sites are within: 0.783 - 5.818

peak=   -4.887 closest distance to " CD  GLN A  58 " =    0.921
peak=   -4.473 closest distance to " O   HOH Z 266 " =    5.469
peak=   -4.466 closest distance to " CD  GLN A 223 " =    1.511
peak=   -4.270 closest distance to " CG2 ILE A  49 " =    2.729
peak=   -4.264 closest distance to " CD1 PHE A  59 " =    2.057
peak=   -4.095 closest distance to " CD  ARG A  14 " =    3.372
peak=   -4.081 closest distance to " O   PRO A 198 " =    1.355
peak=   -4.078 closest distance to " NE2 GLN A 223 " =    1.251
peak=   -4.069 closest distance to " O   HOH Z 166 " =    1.522
peak=   -4.059 closest distance to " CG  GLN A  11 " =    1.352
peak=   -3.995 closest distance to " CD  ARG A 156 " =    2.091
peak=   -3.978 closest distance to " O   HOH Z 150 " =    0.783
peak=   -3.948 closest distance to " O   PHE A 218 " =    1.384
peak=   -3.942 closest distance to " CD2 LEU A 237 " =    2.509
peak=   -3.932 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.930 closest distance to " CB  PRO A 243 " =    2.844
peak=   -3.919 closest distance to " OXT GLY A 302 " =    3.038
peak=   -3.919 closest distance to " O   VAL A  67 " =    2.802
peak=   -3.913 closest distance to " OG  SER A  97 " =    2.233
peak=   -3.895 closest distance to " O   HOH Z 407 " =    1.187
peak=   -3.878 closest distance to " CG1 VAL A 112 " =    2.623
peak=   -3.860 closest distance to " CE2 PHE A  61 " =    2.670
peak=   -3.831 closest distance to " CG  PRO A 243 " =    1.630
peak=   -3.816 closest distance to " CG2 ILE A  20 " =    3.046
peak=   -3.811 closest distance to " O   ALA A  34 " =    2.445
peak=   -3.808 closest distance to " O   HOH Z 155 " =    1.921
peak=   -3.808 closest distance to " C   HIS A 108 " =    1.073
peak=   -3.783 closest distance to " CD  GLN A  88 " =    0.988
peak=   -3.777 closest distance to " CZ  TYR A 169 " =    1.964
peak=   -3.770 closest distance to " O   HOH Z 377 " =    2.252
peak=   -3.764 closest distance to " O   GLN A  11 " =    1.078
peak=   -3.761 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -3.749 closest distance to " O   HOH Z 374 " =    1.988
peak=   -3.725 closest distance to " CD2 PHE A  61 " =    2.084
peak=   -3.725 closest distance to " O   HOH Z 348 " =    2.267
peak=   -3.721 closest distance to " O   SER A 206 " =    1.395
peak=   -3.720 closest distance to " O   HOH Z  56 " =    1.637
peak=   -3.718 closest distance to " N   ALA A  43 " =    2.832
peak=   -3.714 closest distance to " O   HOH Z 422 " =    1.462
peak=   -3.707 closest distance to " CD2 TYR A 293 " =    1.816
peak=   -3.699 closest distance to " O   HOH Z   6 " =    1.439
peak=   -3.683 closest distance to " CE2 TYR A  30 " =    2.689
peak=   -3.678 closest distance to " NH2 ARG A  66 " =    1.960
peak=   -3.672 closest distance to " O   HOH Z 418 " =    1.273
peak=   -3.667 closest distance to " CZ  PHE A  38 " =    2.360
peak=   -3.664 closest distance to " ND2 ASN A  45 " =    1.946
peak=   -3.660 closest distance to " O   ILE A 109 " =    2.639
peak=   -3.654 closest distance to " O   HOH Z   7 " =    1.183
peak=   -3.653 closest distance to " C   THR A 279 " =    1.107
peak=   -3.651 closest distance to " O   HOH Z 109 " =    3.265
peak=   -3.643 closest distance to " O   HOH Z 165 " =    1.855
peak=   -3.643 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.641 closest distance to " CA  GLY A 203 " =    2.375
peak=   -3.635 closest distance to " CA  VAL A 197 " =    0.977
peak=   -3.631 closest distance to " O   HOH Z 392 " =    1.180
peak=   -3.631 closest distance to " CD1 ILE A 109 " =    2.809
peak=   -3.621 closest distance to " NE  ARG A  66 " =    4.677
peak=   -3.614 closest distance to " CB  GLU A 277 " =    1.324
peak=   -3.600 closest distance to " O   VAL A 189 " =    2.565
peak=   -3.583 closest distance to " OE1 GLN A  88 " =    1.052
peak=   -3.581 closest distance to " O   HOH Z 331 " =    1.305
peak=   -3.575 closest distance to " O   TRP A  92 " =    1.995
peak=   -3.566 closest distance to " O   HOH Z  10 " =    1.675
peak=   -3.559 closest distance to " CG  GLU A  53 " =    1.479
peak=   -3.555 closest distance to " O   HOH Z 197 " =    1.954
peak=   -3.551 closest distance to " O   HOH Z 234 " =    4.202
peak=   -3.550 closest distance to " O   HOH Z 231 " =    2.425
peak=   -3.550 closest distance to " CD2 LEU A 237 " =    2.591
peak=   -3.548 closest distance to " OG BSER A 210 " =    1.254
peak=   -3.547 closest distance to " SD  MET A 105 " =    2.443
peak=   -3.541 closest distance to " O   HOH Z 102 " =    1.726
peak=   -3.534 closest distance to " O   HOH Z 171 " =    2.311
peak=   -3.534 closest distance to " OD1 ASP A 171 " =    1.431
peak=   -3.531 closest distance to " NH2 ARG A  79 " =    2.167
peak=   -3.529 closest distance to " O   HOH Z 283 " =    2.087
peak=   -3.523 closest distance to " C   ASN A 285 " =    2.391
peak=   -3.522 closest distance to " O   VAL A 174 " =    2.132
peak=   -3.517 closest distance to " CB  ALA A  10 " =    2.198
peak=   -3.512 closest distance to " OD2 ASP A 171 " =    1.850
peak=   -3.503 closest distance to " CD2 HIS A 115 " =    0.992
peak=   -3.498 closest distance to " OD1 ASN A 148 " =    1.420
peak=   -3.497 closest distance to " CE  LYS A 119 " =    2.146
peak=   -3.497 closest distance to " O   HOH Z 196 " =    2.435
peak=   -3.490 closest distance to " NH2 ARG A 159 " =    2.418
peak=   -3.489 closest distance to " CE3 TRP A 150 " =    2.295
peak=   -3.485 closest distance to " ND2BASN A 224 " =    1.994
peak=   -3.484 closest distance to " CA  SER A 276 " =    1.493
peak=   -3.483 closest distance to " CG2 VAL A 189 " =    2.203
peak=   -3.479 closest distance to " CG1 VAL A  78 " =    2.724
peak=   -3.477 closest distance to " O   HOH Z 221 " =    1.100
peak=   -3.476 closest distance to " O   GLY A  17 " =    1.109
peak=   -3.475 closest distance to " OE1 GLN A 223 " =    2.432
peak=   -3.457 closest distance to " OD1 ASP A 191 " =    1.467
peak=   -3.454 closest distance to " O   HOH Z 136 " =    2.339
peak=   -3.448 closest distance to " O   HOH Z  40 " =    2.918
peak=   -3.441 closest distance to " O   LYS A  76 " =    1.452
peak=   -3.441 closest distance to " ND2 ASN A 187 " =    1.664
peak=   -3.440 closest distance to " O   SER A 276 " =    1.708
peak=   -3.438 closest distance to " O   HOH Z  90 " =    3.799
peak=   -3.428 closest distance to " O   HOH Z  37 " =    1.861
peak=   -3.428 closest distance to " CD1 LEU A  25 " =    2.483
peak=   -3.424 closest distance to " O   HOH Z 118 " =    1.186
peak=   -3.421 closest distance to " O   HOH Z 407 " =    3.597
peak=   -3.419 closest distance to " CD1 LEU A 167 " =    2.021
peak=   -3.415 closest distance to " N   SER A 134 " =    1.255
peak=   -3.415 closest distance to " O   HOH Z 231 " =    2.306
peak=   -3.408 closest distance to " CB  ALA A 131 " =    2.443
peak=   -3.406 closest distance to " CG  ASP A 132 " =    2.388
peak=   -3.406 closest distance to " CB  SER A 210 " =    1.055
peak=   -3.402 closest distance to " O   HOH Z 366 " =    1.809
peak=   -3.402 closest distance to " CB  ALA A  43 " =    2.628
peak=   -3.401 closest distance to " O   HOH Z 149 " =    1.999
peak=   -3.397 closest distance to " O   HOH Z 292 " =    4.584
peak=   -3.396 closest distance to " ND2 ASN A 249 " =    2.319
peak=   -3.394 closest distance to " ND2 ASN A  45 " =    1.169
peak=   -3.394 closest distance to " CD  ARG A 195 " =    5.005
peak=   -3.390 closest distance to " CG  PRO A 280 " =    2.322
peak=   -3.388 closest distance to " O   HOH Z 174 " =    2.133
peak=   -3.385 closest distance to " CG  GLN A 103 " =    2.501
peak=   -3.381 closest distance to " O   HOH Z 198 " =    1.866
peak=   -3.373 closest distance to " O   HOH Z 185 " =    2.515
peak=   -3.372 closest distance to " O   HOH Z 150 " =    1.811
peak=   -3.363 closest distance to " CH2 TRP A 179 " =    1.259
peak=   -3.361 closest distance to " O   HOH Z 397 " =    1.104
peak=   -3.357 closest distance to " CD1 ILE A 263 " =    2.041
peak=   -3.356 closest distance to " CG  LEU A  83 " =    2.074
peak=   -3.355 closest distance to " O   HOH Z  19 " =    2.336
peak=   -3.350 closest distance to " CB  ASP A 162 " =    2.491
peak=   -3.349 closest distance to " CB  PHE A 192 " =    2.101
peak=   -3.349 closest distance to " O   HOH Z  52 " =    1.896
peak=   -3.346 closest distance to " O   HOH Z 351 " =    1.657
peak=   -3.345 closest distance to " CA  GLY A 241 " =    2.368
peak=   -3.344 closest distance to " NE2 GLN A  94 " =    1.850
peak=   -3.341 closest distance to " O   HOH Z  15 " =    1.429
peak=   -3.334 closest distance to " O   HOH Z 252 " =    3.732
peak=   -3.332 closest distance to " O   HOH Z 388 " =    2.068
peak=   -3.328 closest distance to " O   HOH Z 156 " =    3.679
peak=   -3.328 closest distance to " C   VAL A 265 " =    0.876
peak=   -3.323 closest distance to " O   ASP A 171 " =    1.041
peak=   -3.315 closest distance to " CG1 VAL A 112 " =    2.664
peak=   -3.313 closest distance to " OH  TYR A 172 " =    1.879
peak=   -3.310 closest distance to " O   HOH Z 135 " =    1.625
peak=   -3.307 closest distance to " CB  ALA A 291 " =    2.514
peak=   -3.306 closest distance to " CG  MET A 105 " =    0.931
peak=   -3.305 closest distance to " O   HOH Z  71 " =    2.290
peak=   -3.304 closest distance to " OD2 ASP A 298 " =    1.031
peak=   -3.298 closest distance to " CH2 TRP A 150 " =    1.027
peak=   -3.298 closest distance to " OG BSER A 210 " =    2.378
peak=   -3.297 closest distance to " O   HOH Z 155 " =    2.021
peak=   -3.291 closest distance to " O   HOH Z 200 " =    1.165
peak=   -3.276 closest distance to " O   HOH Z 250 " =    1.837
peak=   -3.267 closest distance to " O   PRO A 163 " =    2.111
peak=   -3.265 closest distance to " C   LEU A 143 " =    1.200
peak=   -3.263 closest distance to " CA  ASN A 127 " =    1.062
peak=   -3.262 closest distance to " CA  GLY A 241 " =    3.259
peak=   -3.252 closest distance to " O   HOH Z   2 " =    2.372
peak=   -3.250 closest distance to " CG  ARG A 259 " =    2.444
peak=   -3.247 closest distance to " CE  MET A  93 " =    1.432
peak=   -3.247 closest distance to " O   HOH Z 423 " =    2.486
peak=   -3.237 closest distance to " O   HOH Z 336 " =    5.561
peak=   -3.237 closest distance to " CB  PHE A  16 " =    2.376
peak=   -3.233 closest distance to " O   HOH Z 290 " =    1.212
peak=   -3.229 closest distance to " C   ALA A 158 " =    1.359
peak=   -3.226 closest distance to " O   HOH Z 377 " =    1.088
peak=   -3.224 closest distance to " C   ARG A  79 " =    2.764
peak=   -3.222 closest distance to " CB  ALA A 248 " =    2.110
peak=   -3.216 closest distance to " NE2 GLN A 103 " =    1.723
peak=   -3.215 closest distance to " CD2 PHE A 225 " =    1.298
peak=   -3.212 closest distance to " CG2 ILE A 263 " =    2.354
peak=   -3.208 closest distance to " O   HOH Z 301 " =    2.348
peak=   -3.207 closest distance to " O   HOH Z 275 " =    1.566
peak=   -3.206 closest distance to " CD  GLU A 236 " =    1.110
peak=   -3.205 closest distance to " N   ALA A 248 " =    1.743
peak=   -3.197 closest distance to " O   HOH Z 345 " =    2.991
peak=   -3.196 closest distance to " O   SER A 210 " =    1.785
peak=   -3.193 closest distance to " CD  GLN A  73 " =    0.783
peak=   -3.183 closest distance to " O   ALA A  10 " =    1.803
peak=   -3.178 closest distance to " O   HOH Z 196 " =    1.850
peak=   -3.171 closest distance to " CB  SER A 146 " =    2.173
peak=   -3.170 closest distance to " N   ALA A 226 " =    2.030
peak=   -3.162 closest distance to " OD1 ASN A 187 " =    1.594
peak=   -3.161 closest distance to " CD1 ILE A 106 " =    2.119
peak=   -3.160 closest distance to " O   HOH Z 108 " =    1.985
peak=   -3.158 closest distance to " CG1 VAL A 197 " =    2.229
peak=   -3.156 closest distance to " O   HOH Z 128 " =    2.523
peak=   -3.154 closest distance to " O  BHOH Z 338 " =    1.416
peak=   -3.151 closest distance to " O   HOH Z 252 " =    4.038
peak=   -3.151 closest distance to " O   ARG A 275 " =    2.078
peak=   -3.150 closest distance to " CG  LEU A 281 " =    1.855
peak=   -3.148 closest distance to " ND2 ASN A  39 " =    1.446
peak=   -3.142 closest distance to " CB  ALA A 154 " =    2.744
peak=   -3.140 closest distance to " CG2BVAL A  41 " =    1.433
peak=   -3.135 closest distance to " O   HOH Z 106 " =    2.127
peak=   -3.135 closest distance to " CB  ASN A  45 " =    2.158
peak=   -3.129 closest distance to " O   HOH Z 409 " =    5.221
peak=   -3.126 closest distance to " CD  ARG A  79 " =    1.246
peak=   -3.124 closest distance to " OE1 GLN A  88 " =    1.210
peak=   -3.120 closest distance to " OH  TYR A 169 " =    0.953
peak=   -3.111 closest distance to " CD2 HIS A 207 " =    2.219
peak=   -3.107 closest distance to " OE1 GLN A  89 " =    1.910
peak=   -3.101 closest distance to " O   HOH Z 114 " =    3.641
peak=   -3.093 closest distance to " CD2 TYR A 247 " =    2.372
peak=   -3.092 closest distance to " O   HOH Z 424 " =    2.995
peak=   -3.092 closest distance to " OG1 THR A  82 " =    1.438
peak=   -3.089 closest distance to " O   SER A   3 " =    1.129
peak=   -3.085 closest distance to " OG BSER A 134 " =    1.477
peak=   -3.084 closest distance to " O   HOH Z 149 " =    2.315
peak=   -3.077 closest distance to " O   HOH Z 146 " =    1.265
peak=   -3.076 closest distance to " O   HOH Z  91 " =    2.225
peak=   -3.072 closest distance to " O   HOH Z 191 " =    5.818
peak=   -3.072 closest distance to " CD  ARG A 139 " =    1.522
peak=   -3.069 closest distance to " CD1 ILE A 109 " =    2.042
peak=   -3.050 closest distance to " O   GLY A 196 " =    1.244
peak=   -3.050 closest distance to " N   GLN A  58 " =    1.438
peak=   -3.042 closest distance to " OD2 ASP A 270 " =    1.041
peak=   -3.037 closest distance to " CH2 TRP A 177 " =    2.032

================= 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    :  0.4553 0.4427   6.270554e+00   6.244105e+00
   1_bss:  0.4450 0.4303   6.262532e+00   6.231635e+00
   1_xyz:  0.3534 0.3808   6.111388e+00   6.152516e+00
   1_adp:  0.3256 0.3932   6.063631e+00   6.165927e+00
   1_occ:  0.3252 0.3930   6.062892e+00   6.165835e+00
   2_bss:  0.3245 0.3905   6.064723e+00   6.167810e+00
   2_xyz:  0.2656 0.3236   5.893524e+00   6.036938e+00
   2_adp:  0.2517 0.3134   5.863651e+00   6.015185e+00
   2_occ:  0.2516 0.3132   5.863280e+00   6.015457e+00
   3_bss:  0.2515 0.3128   5.863750e+00   6.015392e+00
   3_xyz:  0.2097 0.2600   5.687548e+00   5.858708e+00
   3_adp:  0.1959 0.2470   5.635930e+00   5.813981e+00
   3_occ:  0.1958 0.2471   5.635376e+00   5.813876e+00
   4_bss:  0.1958 0.2470   5.636355e+00   5.814029e+00
   4_xyz:  0.1497 0.1946   5.388605e+00   5.594231e+00
   4_adp:  0.1380 0.1855   5.320006e+00   5.535310e+00
   4_occ:  0.1379 0.1854   5.319193e+00   5.534609e+00
   5_bss:  0.1380 0.1851   5.319438e+00   5.532749e+00
   5_xyz:  0.1269 0.1736   5.256804e+00   5.480323e+00
   5_adp:  0.1235 0.1727   5.239259e+00   5.469289e+00
   5_occ:  0.1234 0.1727   5.238915e+00   5.469194e+00
   5_bss:  0.1234 0.1726   5.238775e+00   5.469139e+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:  0.283  32.142  -3.720   4.896   1.180   0.000   0.000   0.000
   1_xyz:  0.283  32.142  -3.720   4.896   1.180   0.000   0.000   0.000
   1_adp:  0.283  32.142  -3.720   4.896   1.180   0.000   0.000   0.000
   1_occ:  0.283  32.142  -3.720   4.896   1.180   0.000   0.000   0.000
   2_bss:  0.272  48.425  -1.751   2.882   0.815   0.000   0.000   0.000
   2_xyz:  0.272  48.425  -1.751   2.882   0.815   0.000   0.000   0.000
   2_adp:  0.272  48.425  -1.751   2.882   0.815   0.000   0.000   0.000
   2_occ:  0.272  48.425  -1.751   2.882   0.815   0.000   0.000   0.000
   3_bss:  0.316  61.789  -1.686   1.577   0.381   0.000   0.000   0.000
   3_xyz:  0.316  61.789  -1.686   1.577   0.381   0.000   0.000   0.000
   3_adp:  0.316  61.789  -1.686   1.577   0.381   0.000   0.000   0.000
   3_occ:  0.316  61.789  -1.686   1.577   0.381   0.000   0.000   0.000
   4_bss:  0.328  76.515  -1.873   0.412  -0.061   0.000  -0.000  -0.000
   4_xyz:  0.328  76.515  -1.873   0.412  -0.061   0.000  -0.000  -0.000
   4_adp:  0.328  76.515  -1.873   0.412  -0.061   0.000  -0.000  -0.000
   4_occ:  0.328  76.515  -1.873   0.412  -0.061   0.000  -0.000  -0.000
   5_bss:  0.334  75.142  -1.884  -0.329   0.018  -0.000   0.000   0.000
   5_xyz:  0.334  75.142  -1.884  -0.329   0.018  -0.000   0.000   0.000
   5_adp:  0.334  75.142  -1.884  -0.329   0.018  -0.000   0.000   0.000
   5_occ:  0.334  75.142  -1.884  -0.329   0.018  -0.000   0.000   0.000
   5_bss:  0.328  74.074  -1.671  -0.338   0.249  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.027 0.4965  0.6482    61444.174
   1_bss:  50.842 0.5101  0.6839    58194.378
   1_xyz:  43.612 0.5988  0.7843    43468.260
   1_adp:  44.404 0.5889  0.7714    45103.883
   1_occ:  44.409 0.5888  0.7702    45019.963
   2_bss:  44.124 0.5925  0.7753    44901.048
   2_xyz:  35.245 0.6978  0.8958    29684.052
   2_adp:  33.825 0.7145  0.8965    27771.863
   2_occ:  33.843 0.7144  0.8957    27793.392
   3_bss:  33.764 0.7154  0.8817    27768.054
   3_xyz:  26.814 0.7917  0.9488    17901.682
   3_adp:  24.925 0.8125  0.9514    16136.216
   3_occ:  24.907 0.8126  0.9516    16114.775
   4_bss:  24.851 0.8133  0.9336    16102.389
   4_xyz:  18.802 0.8725  0.9714     9665.057
   4_adp:  17.418 0.8856  0.9691     8723.091
   4_occ:  17.399 0.8857  0.9691     8716.442
   5_bss:  17.349 0.8862  0.9623     8665.029
   5_xyz:  16.093 0.8976  0.9681     7744.828
   5_adp:  15.833 0.9000  0.9614     7620.342
   5_occ:  15.828 0.9000  0.9614     7618.490
   5_bss:  15.826 0.9000  0.9665     7613.941
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6666e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6666e-01
   1_xyz:   1.501  0.011  0.092 15.721  0.005  4.111   1.1730e-01
   1_adp:   1.501  0.011  0.092 15.721  0.005  4.111   1.1730e-01
   1_occ:   1.501  0.011  0.092 15.721  0.005  4.111   1.1730e-01
   2_bss:   1.501  0.011  0.092 15.721  0.005  4.111   1.1730e-01
   2_xyz:   1.379  0.009  0.090 15.184  0.005  4.113   9.6655e-02
   2_adp:   1.379  0.009  0.090 15.184  0.005  4.113   9.6655e-02
   2_occ:   1.379  0.009  0.090 15.184  0.005  4.113   9.6655e-02
   3_bss:   1.379  0.009  0.090 15.184  0.005  4.113   9.6655e-02
   3_xyz:   1.037  0.007  0.066 14.472  0.004  4.123   6.2984e-02
   3_adp:   1.037  0.007  0.066 14.472  0.004  4.123   6.2984e-02
   3_occ:   1.037  0.007  0.066 14.472  0.004  4.123   6.2984e-02
   4_bss:   1.037  0.007  0.066 14.472  0.004  4.123   6.2984e-02
   4_xyz:   1.200  0.010  0.084 14.865  0.004  4.114   8.3404e-02
   4_adp:   1.200  0.010  0.084 14.865  0.004  4.114   8.3404e-02
   4_occ:   1.200  0.010  0.084 14.865  0.004  4.114   8.3404e-02
   5_bss:   1.200  0.010  0.084 14.865  0.004  4.114   8.3404e-02
   5_xyz:   1.070  0.009  0.078 14.635  0.004  4.123   6.7645e-02
   5_adp:   1.070  0.009  0.078 14.635  0.004  4.123   6.7645e-02
   5_occ:   1.070  0.009  0.078 14.635  0.004  4.123   6.7645e-02
   5_bss:   1.070  0.009  0.078 14.635  0.004  4.123   6.7645e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4404e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4404e-01
   1_xyz:   8.721  0.059  0.401 82.704  0.026  1.999   1.0406e-01
   1_adp:   8.721  0.059  0.401 82.704  0.026  1.999   1.0406e-01
   1_occ:   8.721  0.059  0.401 82.704  0.026  1.999   1.0406e-01
   2_bss:   8.721  0.059  0.401 82.704  0.026  1.999   1.0406e-01
   2_xyz:   7.839  0.048  0.302 88.548  0.020  2.216   1.0365e-01
   2_adp:   7.839  0.048  0.302 88.548  0.020  2.216   1.0365e-01
   2_occ:   7.839  0.048  0.302 88.548  0.020  2.216   1.0365e-01
   3_bss:   7.839  0.048  0.302 88.548  0.020  2.216   1.0365e-01
   3_xyz:   6.968  0.036  0.261 82.679  0.051  2.277   6.6777e-02
   3_adp:   6.968  0.036  0.261 82.679  0.051  2.277   6.6777e-02
   3_occ:   6.968  0.036  0.261 82.679  0.051  2.277   6.6777e-02
   4_bss:   6.968  0.036  0.261 82.679  0.051  2.277   6.6777e-02
   4_xyz:   8.550  0.072  0.242 84.157  0.039  2.192   6.0414e-02
   4_adp:   8.550  0.072  0.242 84.157  0.039  2.192   6.0414e-02
   4_occ:   8.550  0.072  0.242 84.157  0.039  2.192   6.0414e-02
   5_bss:   8.550  0.072  0.242 84.157  0.039  2.192   6.0414e-02
   5_xyz:   7.827  0.054  0.262 81.411  0.040  2.367   6.4682e-02
   5_adp:   7.827  0.054  0.262 81.411  0.040  2.367   6.4682e-02
   5_occ:   7.827  0.054  0.262 81.411  0.040  2.367   6.4682e-02
   5_bss:   7.827  0.054  0.262 81.411  0.040  2.367   6.4682e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  97.78   0.00  18.46  77.59   0.00  15.14  97.78   0.00  36.56
   1_occ:  97.78   0.00  18.46  77.59   0.00  15.14  97.78   0.00  36.56
   2_bss:  97.78   0.00  18.46  77.59   0.00  15.14  97.78   0.00  36.56
   2_xyz:  97.78   0.00  18.46  77.59   0.00  15.14  97.78   0.00  36.56
   2_adp:  96.15   0.00  17.76  94.01   0.00  14.24  96.15   0.00  36.93
   2_occ:  96.15   0.00  17.76  94.01   0.00  14.24  96.15   0.00  36.93
   3_bss:  96.15   0.00  17.76  94.01   0.00  14.24  96.15   0.00  36.93
   3_xyz:  96.15   0.00  17.76  94.01   0.00  14.24  96.15   0.00  36.93
   3_adp:  95.00   0.00  17.71  88.83   0.00  13.37  95.00   3.35  41.39
   3_occ:  95.00   0.00  17.71  88.83   0.00  13.37  95.00   3.35  41.39
   4_bss:  95.00   0.00  17.71  88.83   0.00  13.37  95.00   3.35  41.39
   4_xyz:  95.00   0.00  17.71  88.83   0.00  13.37  95.00   3.35  41.39
   4_adp:  95.27   0.00  17.31  91.56   0.35  12.64  95.27   0.00  42.76
   4_occ:  95.27   0.00  17.31  91.56   0.35  12.64  95.27   0.00  42.76
   5_bss:  95.27   0.00  17.31  91.56   0.35  12.64  95.27   0.00  42.76
   5_xyz:  95.27   0.00  17.31  91.56   0.35  12.64  95.27   0.00  42.76
   5_adp: 107.46   0.00  17.36 107.46   0.00  12.38 106.25   0.00  44.51
   5_occ: 107.46   0.00  17.36 107.46   0.00  12.38 106.25   0.00  44.51
   5_bss: 107.46   0.00  17.37 107.46   0.00  12.38 106.25   0.00  44.52
------------------------------------------------------------------------
 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:    1.594    0.017    0.346
   1_adp:    1.594    0.017    0.346
   1_occ:    1.594    0.017    0.346
   2_bss:    1.594    0.017    0.346
   2_xyz:    1.609    0.037    0.526
   2_adp:    1.609    0.037    0.526
   2_occ:    1.609    0.037    0.526
   3_bss:    1.609    0.037    0.526
   3_xyz:    1.452    0.066    0.655
   3_adp:    1.452    0.066    0.655
   3_occ:    1.452    0.066    0.655
   4_bss:    1.452    0.066    0.655
   4_xyz:    1.637    0.041    0.780
   4_adp:    1.637    0.041    0.780
   4_occ:    1.637    0.041    0.780
   5_bss:    1.637    0.041    0.780
   5_xyz:    1.568    0.082    0.808
   5_adp:    1.568    0.082    0.808
   5_occ:    1.568    0.082    0.808
   5_bss:    1.568    0.082    0.808
------------------------------------------------------------------------

CPU time actual refinement: 348.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/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_602/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_602/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.72 
  Macro-tasks:
    bulk solvent and scale       = 49.35  
    individual site refinement   = 143.23 
    weights calculation          = 28.89  
    collect and process          = 6.59   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.17 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 108.84 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 118.49 
    fmodel                         = 7.94   
    r_factors                      = 0.29   
    phase_errors                   = 10.58  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 258.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.916 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    643 calls, 108.61 s
gradients_fft:          588 calls, 105.17 s

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

# Date 2008-01-16 Time 05:13:35 PST -0800 (1200489215.09 s)
Start R-work = 0.4553, R-free = 0.4427 (no bulk solvent and anisotropic scale)
Final R-work = 0.1412, R-free = 0.1872 (no bulk solvent and anisotropic scale)

Start R-work = 0.4450, R-free = 0.4303
Final R-work = 0.1234, R-free = 0.1726