# Date 2008-01-16 Time 05:41:49 PST -0800 (1200490909.59 s)
#phil __OFF__

Command line arguments: "../840.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26173
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 840

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99136
Completeness in resolution range: 0.950507
Completeness with d_max=infinity: 0.947564

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9914

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99136
Completeness in resolution range: 0.950507
Completeness with d_max=infinity: 0.947564

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2607 [2166/2194]  1949   217  10.0%
  bin  2:  4.2607 -  3.3947 [2074/2097]  1865   209  10.1%
  bin  3:  3.3947 -  2.9693 [2045/2070]  1841   204  10.0%
  bin  4:  2.9693 -  2.6996 [2045/2061]  1843   202   9.9%
  bin  5:  2.6996 -  2.5070 [2017/2054]  1812   205  10.2%
  bin  6:  2.5070 -  2.3598 [2001/2035]  1812   189   9.4%
  bin  7:  2.3598 -  2.2420 [1989/2026]  1788   201  10.1%
  bin  8:  2.2420 -  2.1447 [1991/2033]  1785   206  10.3%
  bin  9:  2.1447 -  2.0624 [1988/2023]  1796   192   9.7%
  bin 10:  2.0624 -  1.9914 [1273/2016]  1139   134  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/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: 0.12 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:
        1.60 -     2.26: 9
        2.26 -     2.92: 1461
        2.92 -     3.58: 4422
        3.58 -     4.24: 9089
        4.24 -     4.90: 13010
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.599 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.687 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.734 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.860 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27986 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_840/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/model_refine_001.geo

CPU time processing inputs: 8.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4138   r_free= 0.3957   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.233895                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.3464 0.3732      6.5108      6.5177|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.3607 0.3778      6.7856      6.7534|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.3831 0.3395      6.6127      6.5534|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.3955 0.3834      6.4648      6.3796|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.4283 0.3857      6.3284      6.3162|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.4515 0.3769      6.2616      6.0753|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.4438 0.3842      6.2026        6.09|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.4513 0.4466       6.122       6.171|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.4586 0.4539      6.0816       6.068|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.4411 0.4008      6.0498      5.9777|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.4614 0.4084      6.0168      5.9527|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.4496 0.4622      5.9254      5.9774|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.4522 0.4303      5.8231      5.8112|
| 14:  2.0410 -  1.9914 0.50    642   73 0.4177 0.4361      5.7738      5.7052|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.70  34.03   0.83     0.74      71026.47|
|  2:  4.7520 -  3.7918  1361   145  0.75  31.05   0.92     0.82      83877.34|
|  3:  3.7918 -  3.3184  1320   154  0.69  36.55   0.92     0.84      84136.29|
|  4:  3.3184 -  3.0176  1328   144  0.65  40.18   0.93     0.81      70327.19|
|  5:  3.0176 -  2.8028  1298   145  0.60  44.13   0.91     0.79      55443.13|
|  6:  2.8028 -  2.6385  1304   145  0.61  43.56   0.91     0.78      43463.47|
|  7:  2.6385 -  2.5070  1298   146  0.60  43.65   0.94     0.78      39543.99|
|  8:  2.5070 -  2.3983  1298   145  0.56  47.07   0.93     0.76      39113.34|
|  9:  2.3983 -  2.3063  1283   136  0.55  48.19   0.94     0.75      37997.39|
| 10:  2.3063 -  2.2270  1278   146  0.56  47.68   0.97     0.76      34726.12|
| 11:  2.2270 -  2.1576  1275   142  0.56  47.70   0.96     0.79      31729.60|
| 12:  2.1576 -  2.0961  1268   142  0.54  49.14   0.98     0.77      30059.06|
| 13:  2.0961 -  2.0410  1276   138  0.49  52.68   0.95     0.72      27259.57|
| 14:  2.0410 -  1.9914   642    73  0.49  53.02   1.01     0.66      23722.21|
|alpha:            min =        0.66 max =            0.84 mean =         0.77|
|beta:             min =    23722.21 max =        84136.29 mean =     49380.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.71|
|phase err.(test): min =        0.00 max =           89.64 mean =        43.70|
|-----------------------------------------------------------------------------|

============================== 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 = 7.021446              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.828   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.259978              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.542   (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 |  1.599 -  1.929:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.929 -  2.259:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.259 -  2.589:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.589 -  2.919:     1430 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.919 -  3.250:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.250 -  3.580:     2531 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.580 -  3.910:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.910 -  4.240:     4417 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.240 -  4.570:     5909 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.570 -  4.900:     7101 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| 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  1.599 |       0.255 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    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 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4138   r_free= 0.3957   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.233895                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3994   r_free= 0.3809   ksol= 0.29   Bsol= 27.82   scale= 0.937   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,6.07,-1.82,0.00,-0.00,-0.00); trace/3= 0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.218893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.505964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.384   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.656031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.433   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3994      final r-factor (work) = 0.3330          |
| start r-factor (free) = 0.3809      final r-factor (free) = 0.3613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3971 = 6.51 * 0.50 * 6.2183 + 1.00 * 0.1692                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9118 = 6.51 * 0.50 * 6.0886 + 1.00 * 0.1057                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3330      final r-factor (work) = 0.3087          |
| start r-factor (free) = 0.3613      final r-factor (free) = 0.3687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0003 = 0.66 * 1.00 * 6.0886 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9706 = 0.66 * 1.00 * 6.0295 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.41   17.34    None  None   None       |
|    all(noH): 2823   0      0.00    85.41   17.34    None  None   None       |
|    Sol.    : 438    0      2.15    85.41   34.27    None  None   None       |
|    Mac.    : 2385   0      0.00    80.97   14.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.541:  814   |   5:    42.704 -  51.245:   91        |
|      1:     8.541 -  17.082:  924   |   6:    51.245 -  59.786:   48        |
|      2:    17.082 -  25.623:  514   |   7:    59.786 -  68.327:   27        |
|      3:    25.623 -  34.164:  254   |   8:    68.327 -  76.868:   10        |
|      4:    34.164 -  42.704:  137   |   9:    76.868 -  85.409:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3087 r_free = 0.3687             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3084 r_free = 0.3682             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3084   r_free= 0.3682   ksol= 0.29   Bsol= 27.82   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,6.07,-1.82,0.00,-0.00,-0.00); trace/3= 0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.033529                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3073   r_free= 0.3663   ksol= 0.30   Bsol= 42.30   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,3.44,-0.67,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.035111                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.140654              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.109  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687878              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.893   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3073      final r-factor (work) = 0.2536          |
| start r-factor (free) = 0.3663      final r-factor (free) = 0.3036          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6259 = 6.14 * 0.50 * 6.0320 + 1.00 * 0.1057                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3469 = 6.14 * 0.50 * 5.9470 + 1.00 * 0.0877                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2536      final r-factor (work) = 0.2379          |
| start r-factor (free) = 0.3036      final r-factor (free) = 0.2991          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1040 = 0.69 * 1.00 * 5.9470 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0197 = 0.69 * 1.00 * 5.8232 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.67   17.62    None  None   None       |
|    all(noH): 2823   0      0.00    89.67   17.62    None  None   None       |
|    Sol.    : 438    0      0.89    86.25   37.47    None  None   None       |
|    Mac.    : 2385   0      0.00    89.67   13.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.967:  934   |   5:    44.836 -  53.803:  111        |
|      1:     8.967 -  17.934:  921   |   6:    53.803 -  62.770:   58        |
|      2:    17.934 -  26.902:  397   |   7:    62.770 -  71.737:   26        |
|      3:    26.902 -  35.869:  236   |   8:    71.737 -  80.705:   14        |
|      4:    35.869 -  44.836:  119   |   9:    80.705 -  89.672:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2379 r_free = 0.2991             target_work(ml) = 5.820         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2377 r_free = 0.2990             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2377   r_free= 0.2990   ksol= 0.30   Bsol= 42.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,3.44,-0.67,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.819123                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2376   r_free= 0.2978   ksol= 0.31   Bsol= 58.91   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,2.02,-0.21,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.818334                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.522421              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.916   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.621921              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.466  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2376      final r-factor (work) = 0.1863          |
| start r-factor (free) = 0.2978      final r-factor (free) = 0.2381          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1684 = 5.52 * 0.50 * 5.8238 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8544 = 5.52 * 0.50 * 5.7134 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1863      final r-factor (work) = 0.1704          |
| start r-factor (free) = 0.2381      final r-factor (free) = 0.2206          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5675 = 0.62 * 1.00 * 5.7134 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4611 = 0.62 * 1.00 * 5.5450 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.57   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    93.57   17.27    None  None   None       |
|    Sol.    : 438    0      4.33    89.70   41.08    None  None   None       |
|    Mac.    : 2385   0      0.00    93.57   12.90    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 -   9.357: 1100   |   5:    46.783 -  56.140:  101        |
|      1:     9.357 -  18.713:  966   |   6:    56.140 -  65.496:   68        |
|      2:    18.713 -  28.070:  266   |   7:    65.496 -  74.853:   22        |
|      3:    28.070 -  37.426:  147   |   8:    74.853 -  84.209:   16        |
|      4:    37.426 -  46.783:  127   |   9:    84.209 -  93.566:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1704 r_free = 0.2206             target_work(ml) = 5.511         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1703 r_free = 0.2205             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1703   r_free= 0.2205   ksol= 0.31   Bsol= 58.91   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,2.02,-0.21,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.510266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1701   r_free= 0.2203   ksol= 0.33   Bsol= 70.09   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,0.60,-0.41,0.00,-0.00,-0.00); trace/3= -0.41                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.509907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.897751              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.644641              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.543  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1701      final r-factor (work) = 0.1427          |
| start r-factor (free) = 0.2203      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1157 = 2.90 * 0.50 * 5.5471 + 1.00 * 0.0786                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9388 = 2.90 * 0.50 * 5.4335 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1427      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5152 = 0.64 * 1.00 * 5.4335 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4434 = 0.64 * 1.00 * 5.3224 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    103.92  17.02    None  None   None       |
|    all(noH): 2823   0      0.39    103.92  17.02    None  None   None       |
|    Sol.    : 438    0      1.91    100.38  42.86    None  None   None       |
|    Mac.    : 2385   0      0.39    103.92  12.27    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:     0.388 -  10.742: 1392   |   5:    52.156 -  62.510:   83        |
|      1:    10.742 -  21.096:  833   |   6:    62.510 -  72.863:   53        |
|      2:    21.096 -  31.449:  192   |   7:    72.863 -  83.217:   25        |
|      3:    31.449 -  41.803:  121   |   8:    83.217 -  93.570:   10        |
|      4:    41.803 -  52.156:  109   |   9:    93.570 - 103.924:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1344 r_free = 0.1814             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1343 r_free = 0.1814             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1814   ksol= 0.33   Bsol= 70.09   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,0.60,-0.41,0.00,-0.00,-0.00); trace/3= -0.41                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.300114                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1345   r_free= 0.1818   ksol= 0.33   Bsol= 69.02   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,0.02,-0.29,0.00,-0.00,-0.00); trace/3= -0.56                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301602                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.653676              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.509  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.199211              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.944  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1345      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1818      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4676 = 1.65 * 0.50 * 5.3230 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4180 = 1.65 * 0.50 * 5.2773 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1750      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0636 = 0.20 * 1.00 * 5.2773 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0577 = 0.20 * 1.00 * 5.2594 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    100.41  16.45    None  None   None       |
|    all(noH): 2823   0      0.72    100.41  16.45    None  None   None       |
|    Sol.    : 438    0      3.91    99.28   41.02    None  None   None       |
|    Mac.    : 2385   0      0.72    100.41  11.93    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:     0.720 -  10.690: 1417   |   5:    50.567 -  60.537:   82        |
|      1:    10.690 -  20.659:  840   |   6:    60.537 -  70.506:   54        |
|      2:    20.659 -  30.628:  170   |   7:    70.506 -  80.476:   21        |
|      3:    30.628 -  40.598:  121   |   8:    80.476 -  90.445:    8        |
|      4:    40.598 -  50.567:  104   |   9:    90.445 - 100.414:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1717             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1715             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1715   ksol= 0.33   Bsol= 69.02   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,0.02,-0.29,0.00,-0.00,-0.00); trace/3= -0.56                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248243                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.1016 0.1313      5.4056      5.5687|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.0906 0.1105      5.4786      5.6651|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.1149 0.1633      5.5481      5.8916|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.1406 0.1781      5.5544      5.7113|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.1538 0.1858       5.454      5.6033|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.1475 0.2156      5.3508      5.5618|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.1422 0.1901      5.2795      5.5077|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.1388 0.1884      5.1963      5.3756|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.1379 0.1933      5.1436      5.4088|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.1352 0.1928      5.0899      5.3021|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.1314 0.1939      5.0245      5.3231|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.1283 0.1672      4.9643      5.1532|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.1374 0.2030      4.9019      5.1941|
| 14:  2.0410 -  1.9914 0.50    642   73 0.1282 0.1935      4.8022      4.9892|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.94   9.37   0.96     0.93       7355.54|
|  2:  4.7520 -  3.7918  1361   145  0.95   8.68   1.00     0.99       9768.58|
|  3:  3.7918 -  3.3184  1320   154  0.93  12.44   1.02     1.01      11926.21|
|  4:  3.3184 -  3.0176  1328   144  0.90  15.58   1.00     0.97      12108.07|
|  5:  3.0176 -  2.8028  1298   145  0.88  18.05   1.00     0.98      10417.42|
|  6:  2.8028 -  2.6385  1304   145  0.88  18.20   0.98     0.95       8828.50|
|  7:  2.6385 -  2.5070  1298   146  0.89  17.45   0.99     0.95       7560.26|
|  8:  2.5070 -  2.3983  1298   145  0.89  17.71   1.00     0.96       6823.75|
|  9:  2.3983 -  2.3063  1283   136  0.89  17.62   0.99     0.95       6049.45|
| 10:  2.3063 -  2.2270  1278   146  0.89  17.72   0.99     0.95       5553.28|
| 11:  2.2270 -  2.1576  1275   142  0.89  17.58   0.98     0.93       4860.12|
| 12:  2.1576 -  2.0961  1268   142  0.90  16.64   0.99     0.98       4509.89|
| 13:  2.0961 -  2.0410  1276   138  0.89  18.02   0.98     0.98       4002.02|
| 14:  2.0410 -  1.9914   642    73  0.89  17.45   0.96     0.92       3290.61|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3290.61 max =        12108.07 mean =      7550.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.53 mean =        15.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1715   ksol= 0.32   Bsol= 65.47   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.21,-0.24,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248139                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1715   ksol= 0.32   Bsol= 65.47   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.21,-0.24,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248139                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7520 0.99   1401  158 0.1014 0.1311      5.4041       5.567|
|  2:  4.7520 -  3.7918 0.99   1361  145 0.0904 0.1105       5.477      5.6631|
|  3:  3.7918 -  3.3184 0.99   1320  154 0.1150 0.1631      5.5478      5.8921|
|  4:  3.3184 -  3.0176 0.99   1328  144 0.1407 0.1781      5.5549      5.7111|
|  5:  3.0176 -  2.8028 0.98   1298  145 0.1539 0.1860      5.4543      5.6038|
|  6:  2.8028 -  2.6385 0.99   1304  145 0.1475 0.2150      5.3506      5.5604|
|  7:  2.6385 -  2.5070 0.99   1298  146 0.1421 0.1902      5.2794      5.5078|
|  8:  2.5070 -  2.3983 0.99   1298  145 0.1387 0.1885      5.1969      5.3761|
|  9:  2.3983 -  2.3063 0.99   1283  136 0.1377 0.1936      5.1435      5.4099|
| 10:  2.3063 -  2.2270 0.98   1278  146 0.1352 0.1931      5.0905      5.3029|
| 11:  2.2270 -  2.1576 0.98   1275  142 0.1314 0.1940      5.0244      5.3233|
| 12:  2.1576 -  2.0961 0.99   1268  142 0.1283 0.1678      4.9645      5.1548|
| 13:  2.0961 -  2.0410 0.96   1276  138 0.1375 0.2028      4.9026      5.1937|
| 14:  2.0410 -  1.9914 0.50    642   73 0.1282 0.1930      4.8016      4.9873|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7520  1401   158  0.94   9.36   0.96     0.93       7328.07|
|  2:  4.7520 -  3.7918  1361   145  0.95   8.66   1.00     0.99       9733.74|
|  3:  3.7918 -  3.3184  1320   154  0.93  12.42   1.01     1.01      11900.63|
|  4:  3.3184 -  3.0176  1328   144  0.90  15.58   1.00     0.97      12119.76|
|  5:  3.0176 -  2.8028  1298   145  0.88  18.03   1.00     0.98      10404.77|
|  6:  2.8028 -  2.6385  1304   145  0.88  18.18   0.98     0.95       8822.42|
|  7:  2.6385 -  2.5070  1298   146  0.89  17.44   0.99     0.95       7559.62|
|  8:  2.5070 -  2.3983  1298   145  0.89  17.73   0.99     0.96       6840.65|
|  9:  2.3983 -  2.3063  1283   136  0.89  17.63   0.99     0.94       6063.27|
| 10:  2.3063 -  2.2270  1278   146  0.88  17.74   0.99     0.95       5563.34|
| 11:  2.2270 -  2.1576  1275   142  0.89  17.58   0.98     0.93       4862.53|
| 12:  2.1576 -  2.0961  1268   142  0.90  16.66   0.99     0.97       4518.44|
| 13:  2.0961 -  2.0410  1276   138  0.89  18.01   0.98     0.98       3999.68|
| 14:  2.0410 -  1.9914   642    73  0.89  17.43   0.96     0.92       3280.38|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3280.38 max =        12119.76 mean =      7546.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.62 mean =        15.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.168)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    100.39  16.42    None  None   None       |
|    all(noH): 2823   0      0.70    100.39  16.42    None  None   None       |
|    Sol.    : 438    0      3.88    99.26   41.00    None  None   None       |
|    Mac.    : 2385   0      0.70    100.39  11.91    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:     0.696 -  10.666: 1417   |   5:    50.543 -  60.513:   82        |
|      1:    10.666 -  20.635:  840   |   6:    60.513 -  70.482:   54        |
|      2:    20.635 -  30.604:  170   |   7:    70.482 -  80.452:   21        |
|      3:    30.604 -  40.574:  121   |   8:    80.452 -  90.421:    8        |
|      4:    40.574 -  50.543:  104   |   9:    90.421 - 100.390:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 353         
Filter by distance & map next to the model:
   mapped sites are within: 0.638 - 4.957
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 353
   mapped sites are within: 0.700 - 4.957

peak=    5.608 closest distance to " O   HOH Z 210 " =    1.421
peak=    5.354 closest distance to " O   HOH Z 111 " =    2.337
peak=    5.292 closest distance to " CB  GLN A 223 " =    1.366
peak=    5.271 closest distance to " CB  SER A  63 " =    1.273
peak=    5.204 closest distance to " O   PRO A 198 " =    1.613
peak=    5.105 closest distance to " O   HOH Z 134 " =    1.960
peak=    4.951 closest distance to " O   HOH Z 433 " =    1.782
peak=    4.920 closest distance to " CG  PRO A 280 " =    0.907
peak=    4.842 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.818 closest distance to " O   HOH Z 120 " =    0.986
peak=    4.804 closest distance to " CG  PRO A 213 " =    1.321
peak=    4.685 closest distance to " CB  ARG A 275 " =    0.843
peak=    4.681 closest distance to " CG  PRO A  90 " =    1.276
peak=    4.668 closest distance to " CA  TYR A  30 " =    0.953
peak=    4.479 closest distance to " O   HOH Z 133 " =    2.215
peak=    4.475 closest distance to " O   HOH Z 422 " =    0.987
peak=    4.474 closest distance to " CB  ARG A 190 " =    1.817
peak=    4.468 closest distance to " O   HOH Z  80 " =    2.045
peak=    4.437 closest distance to " CB  GLU A 128 " =    1.110
peak=    4.383 closest distance to " O   HOH Z 234 " =    3.781
peak=    4.319 closest distance to " O   HOH Z 209 " =    2.266
peak=    4.262 closest distance to " O   HOH Z 357 " =    2.188
peak=    4.261 closest distance to " O   HOH Z 247 " =    1.545
peak=    4.210 closest distance to " O   HOH Z 130 " =    2.746
peak=    4.201 closest distance to " O   HOH Z 412 " =    3.316
peak=    4.199 closest distance to " O   HOH Z  15 " =    2.004
peak=    4.177 closest distance to " O   HOH Z 418 " =    1.894
peak=    4.176 closest distance to " O   HOH Z 250 " =    2.448
peak=    4.159 closest distance to " O   HOH Z 189 " =    2.333
peak=    4.139 closest distance to " CG2BVAL A  41 " =    0.954
peak=    4.133 closest distance to " O   HOH Z  40 " =    1.977
peak=    4.120 closest distance to " CB  GLN A 183 " =    1.308
peak=    4.116 closest distance to " NH2 ARG A 156 " =    1.223
peak=    4.108 closest distance to " CB  TRP A 266 " =    1.018
peak=    4.099 closest distance to " O   HOH Z 403 " =    1.879
peak=    4.097 closest distance to " O   THR A 251 " =    1.309
peak=    4.087 closest distance to " CB  PRO A  54 " =    0.710
peak=    4.074 closest distance to " O   HOH Z 265 " =    2.069
peak=    4.061 closest distance to " CG  GLN A  77 " =    0.822
peak=    4.034 closest distance to " O   HOH Z 196 " =    1.737
peak=    4.028 closest distance to " O   HOH Z 214 " =    1.433
peak=    4.027 closest distance to " O   HOH Z   7 " =    0.917
peak=    4.012 closest distance to " CB  SER A 141 " =    1.020
peak=    4.010 closest distance to " CG1 ILE A  33 " =    1.344
peak=    3.991 closest distance to " CB  SER A  62 " =    0.843
peak=    3.989 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.966 closest distance to " O   HOH Z 369 " =    2.000
peak=    3.964 closest distance to " O   HOH Z  44 " =    1.929
peak=    3.958 closest distance to " O   HOH Z  47 " =    1.480
peak=    3.951 closest distance to " CD  ARG A 269 " =    0.967
peak=    3.950 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.931 closest distance to " O   GLY A  23 " =    2.386
peak=    3.931 closest distance to " O   HOH Z 128 " =    2.134
peak=    3.928 closest distance to " OD1 ASN A 301 " =    1.117
peak=    3.927 closest distance to " CB  ASN A 148 " =    1.334
peak=    3.924 closest distance to " O   HOH Z 428 " =    1.162
peak=    3.924 closest distance to " O   HOH Z 431 " =    1.313
peak=    3.915 closest distance to " CB  ARG A  79 " =    1.294
peak=    3.913 closest distance to " O   HOH Z 126 " =    1.647
peak=    3.913 closest distance to " CB  LEU A 228 " =    1.181
peak=    3.912 closest distance to " CB  VAL A 202 " =    1.490
peak=    3.900 closest distance to " CA  ALA A  51 " =    0.962
peak=    3.886 closest distance to " O   HOH Z  20 " =    1.730
peak=    3.880 closest distance to " O   HOH Z 426 " =    1.283
peak=    3.875 closest distance to " OE1 GLN A  11 " =    2.055
peak=    3.871 closest distance to " O   HOH Z 389 " =    2.074
peak=    3.861 closest distance to " O   HOH Z  11 " =    1.311
peak=    3.851 closest distance to " CG2 VAL A 197 " =    1.187
peak=    3.845 closest distance to " CD  LYS A 166 " =    1.481
peak=    3.838 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.828 closest distance to " NE2 GLN A  11 " =    1.016
peak=    3.814 closest distance to " O   HOH Z 298 " =    2.002
peak=    3.808 closest distance to " N   ASN A  39 " =    1.209
peak=    3.796 closest distance to " O   HOH Z 394 " =    1.765
peak=    3.789 closest distance to " O   HOH Z 402 " =    1.595
peak=    3.779 closest distance to " CG1 ILE A 120 " =    1.082
peak=    3.775 closest distance to " O   HOH Z 132 " =    2.796
peak=    3.774 closest distance to " CG2 THR A 221 " =    0.984
peak=    3.761 closest distance to " NE2 HIS A 115 " =    1.121
peak=    3.750 closest distance to " CD2 TRP A 179 " =    1.284
peak=    3.749 closest distance to " O   HOH Z 271 " =    2.611
peak=    3.742 closest distance to " CZ  PHE A 218 " =    1.087
peak=    3.741 closest distance to " O   HOH Z  67 " =    2.012
peak=    3.740 closest distance to " O   HOH Z 406 " =    1.563
peak=    3.739 closest distance to " O   HOH Z  63 " =    1.774
peak=    3.719 closest distance to " CA  ARG A 195 " =    1.067
peak=    3.715 closest distance to " O   HOH Z 425 " =    1.491
peak=    3.712 closest distance to " CA  SER A  12 " =    1.501
peak=    3.704 closest distance to " CB  GLU A 277 " =    3.793
peak=    3.700 closest distance to " O   HOH Z 437 " =    1.776
peak=    3.683 closest distance to " CA  ASP A 191 " =    0.847
peak=    3.683 closest distance to " CB  PRO A 198 " =    0.936
peak=    3.682 closest distance to " CG2 THR A 220 " =    0.779
peak=    3.677 closest distance to " CA  ILE A 106 " =    0.746
peak=    3.674 closest distance to " O   HOH Z 155 " =    3.230
peak=    3.669 closest distance to " O   HOH Z 203 " =    1.843
peak=    3.667 closest distance to " CD2 LEU A 297 " =    0.979
peak=    3.666 closest distance to " O   HOH Z 124 " =    1.261
peak=    3.664 closest distance to " O   SER A  87 " =    2.286
peak=    3.662 closest distance to " O   HOH Z 404 " =    1.594
peak=    3.652 closest distance to " O   GLY A  91 " =    1.133
peak=    3.652 closest distance to " O   HOH Z 432 " =    1.854
peak=    3.650 closest distance to " CG2 ILE A  20 " =    1.375
peak=    3.642 closest distance to " O   HOH Z 154 " =    1.392
peak=    3.640 closest distance to " O   HOH Z 174 " =    2.147
peak=    3.637 closest distance to " O   HOH Z  48 " =    2.004
peak=    3.637 closest distance to " CB  MET A 105 " =    1.198
peak=    3.635 closest distance to " OG  SER A  62 " =    2.947
peak=    3.628 closest distance to " O   HOH Z 423 " =    1.876
peak=    3.627 closest distance to " O   HOH Z  88 " =    1.626
peak=    3.626 closest distance to " OD1 ASN A  69 " =    2.473
peak=    3.623 closest distance to " O   HOH Z 133 " =    1.463
peak=    3.621 closest distance to " CA  GLY A 196 " =    0.894
peak=    3.618 closest distance to " CB  GLN A  88 " =    1.107
peak=    3.618 closest distance to " O   HOH Z 193 " =    1.988
peak=    3.617 closest distance to " O   HOH Z 339 " =    1.367
peak=    3.609 closest distance to " CA  ASN A 176 " =    1.302
peak=    3.608 closest distance to " O   VAL A  72 " =    1.390
peak=    3.608 closest distance to " O   HOH Z 258 " =    2.295
peak=    3.608 closest distance to " NH2BARG A 145 " =    2.004
peak=    3.604 closest distance to " O   HOH Z 368 " =    3.334
peak=    3.604 closest distance to " CG2 VAL A  78 " =    1.045
peak=    3.595 closest distance to " CG  PRO A 243 " =    1.216
peak=    3.592 closest distance to " O   HOH Z  78 " =    2.223
peak=    3.592 closest distance to " CB  GLU A 152 " =    1.215
peak=    3.589 closest distance to " CA  ALA A  21 " =    1.408
peak=    3.587 closest distance to " ND2 ASN A 301 " =    1.091
peak=    3.586 closest distance to " CD  ARG A 195 " =    1.039
peak=    3.586 closest distance to " O   HOH Z 291 " =    1.460
peak=    3.585 closest distance to " CD1 LEU A 300 " =    1.243
peak=    3.574 closest distance to " CB  ASN A 285 " =    0.831
peak=    3.570 closest distance to " CB  GLU A 277 " =    0.839
peak=    3.568 closest distance to " O   HOH Z  49 " =    0.979
peak=    3.566 closest distance to " NH1 ARG A  14 " =    1.251
peak=    3.562 closest distance to " O   HOH Z  22 " =    2.730
peak=    3.558 closest distance to " N   THR A  52 " =    1.138
peak=    3.557 closest distance to " CB  ASN A 187 " =    1.187
peak=    3.552 closest distance to " O   HOH Z 377 " =    1.333
peak=    3.549 closest distance to " CB  PRO A 243 " =    1.237
peak=    3.548 closest distance to " CD1 LEU A 222 " =    0.899
peak=    3.545 closest distance to " O   HOH Z 163 " =    1.721
peak=    3.543 closest distance to " O   HOH Z 371 " =    3.304
peak=    3.542 closest distance to " O   HOH Z 435 " =    1.793
peak=    3.542 closest distance to " O  BHOH Z 338 " =    1.070
peak=    3.541 closest distance to " N   ILE A  33 " =    1.046
peak=    3.541 closest distance to " N   SER A 164 " =    0.963
peak=    3.540 closest distance to " NH1 ARG A 269 " =    0.768
peak=    3.540 closest distance to " OE1 GLU A   2 " =    1.673
peak=    3.537 closest distance to " CB  PHE A 283 " =    0.881
peak=    3.535 closest distance to " CB  ASN A  39 " =    0.854
peak=    3.533 closest distance to " CB  TYR A 169 " =    0.787
peak=    3.532 closest distance to " O   HOH Z 261 " =    1.866
peak=    3.531 closest distance to " CB  ASN A 142 " =    1.190
peak=    3.524 closest distance to " CA  SER A  87 " =    0.969
peak=    3.522 closest distance to " O   HOH Z 345 " =    1.663
peak=    3.520 closest distance to " O   HOH Z 395 " =    1.439
peak=    3.516 closest distance to " O   HOH Z 130 " =    1.207
peak=    3.515 closest distance to " CG2 THR A  42 " =    0.914
peak=    3.512 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.512 closest distance to " CA  ALA A 160 " =    1.021
peak=    3.511 closest distance to " O   HOH Z  88 " =    3.502
peak=    3.510 closest distance to " CZ3 TRP A  85 " =    0.984
peak=    3.506 closest distance to " O   HOH Z 227 " =    1.677
peak=    3.505 closest distance to " CA  ASP A 124 " =    0.813
peak=    3.502 closest distance to " O   HOH Z 387 " =    2.664
peak=    3.498 closest distance to " CD  ARG A 159 " =    0.837
peak=    3.495 closest distance to " O   HOH Z 373 " =    1.684
peak=    3.495 closest distance to " OG  SER A 245 " =    1.623
peak=    3.493 closest distance to " CD  ARG A  36 " =    1.030
peak=    3.492 closest distance to " CA  VAL A  41 " =    0.830
peak=    3.490 closest distance to " O   HOH Z  21 " =    1.895
peak=    3.488 closest distance to " O   HOH Z 142 " =    1.316
peak=    3.481 closest distance to " CA  PRO A  90 " =    1.004
peak=    3.477 closest distance to " CA  GLN A  88 " =    1.262
peak=    3.476 closest distance to " CA  THR A 246 " =    1.051
peak=    3.466 closest distance to " CG AARG A 275 " =    1.138
peak=    3.466 closest distance to " O   HOH Z 368 " =    1.893
peak=    3.465 closest distance to " OH  TYR A 169 " =    0.953
peak=    3.460 closest distance to " CB  GLN A 194 " =    0.971
peak=    3.455 closest distance to " CZ  PHE A  38 " =    1.322
peak=    3.455 closest distance to " ND2 ASN A 187 " =    1.546
peak=    3.454 closest distance to " CB  ASP A 140 " =    0.763
peak=    3.450 closest distance to " O   HOH Z 344 " =    3.230
peak=    3.442 closest distance to " CB  MET A  47 " =    0.976
peak=    3.442 closest distance to " O   HOH Z 118 " =    1.302
peak=    3.440 closest distance to " CA  LYS A 117 " =    1.309
peak=    3.438 closest distance to " CA  ALA A 295 " =    1.121
peak=    3.437 closest distance to " O   HOH Z 336 " =    1.559
peak=    3.436 closest distance to " CG  GLN A  11 " =    1.146
peak=    3.432 closest distance to " CA  GLU A 152 " =    0.935
peak=    3.430 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.428 closest distance to " CB  ALA A 256 " =    1.370
peak=    3.428 closest distance to " CB  MET A  40 " =    0.781
peak=    3.424 closest distance to " O   HOH Z 303 " =    2.179
peak=    3.424 closest distance to " O   HOH Z 126 " =    2.162
peak=    3.423 closest distance to " O   HOH Z  30 " =    1.658
peak=    3.421 closest distance to " CE  LYS A 119 " =    1.104
peak=    3.421 closest distance to " CA  ASN A 215 " =    1.180
peak=    3.417 closest distance to " CA  ALA A 100 " =    1.311
peak=    3.411 closest distance to " O   HOH Z 380 " =    1.755
peak=    3.403 closest distance to " O   HOH Z 374 " =    2.689
peak=    3.402 closest distance to " CB  GLU A  46 " =    1.040
peak=    3.401 closest distance to " O   SER A  26 " =    1.628
peak=    3.400 closest distance to " CE1 HIS A 108 " =    1.189
peak=    3.396 closest distance to " C   ILE A 106 " =    1.841
peak=    3.396 closest distance to " O   HOH Z 176 " =    1.643
peak=    3.394 closest distance to " O   HOH Z 128 " =    2.020
peak=    3.391 closest distance to " CB  GLN A  58 " =    0.952
peak=    3.390 closest distance to " O   ALA A 165 " =    1.365
peak=    3.387 closest distance to " CG  ARG A  66 " =    0.937
peak=    3.380 closest distance to " O   HOH Z 154 " =    2.444
peak=    3.379 closest distance to " O   HOH Z 250 " =    1.523
peak=    3.375 closest distance to " CA  LEU A  83 " =    1.428
peak=    3.372 closest distance to " CD AARG A 275 " =    1.484
peak=    3.370 closest distance to " O   GLN A  11 " =    1.017
peak=    3.369 closest distance to " OG1 THR A 294 " =    2.442
peak=    3.368 closest distance to " NE1 TRP A 274 " =    0.757
peak=    3.363 closest distance to " O   HOH Z  90 " =    3.382
peak=    3.362 closest distance to " CG1 VAL A 153 " =    1.079
peak=    3.361 closest distance to " O   HOH Z 102 " =    1.266
peak=    3.360 closest distance to " O   HOH Z 284 " =    3.028
peak=    3.358 closest distance to " O   HOH Z 146 " =    1.573
peak=    3.355 closest distance to " CB  ALA A  71 " =    1.246
peak=    3.353 closest distance to " O   HOH Z 409 " =    3.197
peak=    3.350 closest distance to " CB  ALA A  34 " =    0.700
peak=    3.349 closest distance to " CA  GLN A 223 " =    0.831
peak=    3.340 closest distance to " ND2 ASN A  45 " =    1.429
peak=    3.335 closest distance to " CA  ILE A 263 " =    0.991
peak=    3.331 closest distance to " O   HOH Z  48 " =    1.580
peak=    3.330 closest distance to " O   ALA A 158 " =    1.212
peak=    3.329 closest distance to " CB  GLN A  73 " =    1.010
peak=    3.327 closest distance to " O   HOH Z 109 " =    2.072
peak=    3.323 closest distance to " CB  SER A   3 " =    1.360
peak=    3.323 closest distance to " CB  ALA A 291 " =    1.090
peak=    3.323 closest distance to " CA  ASP A 162 " =    1.187
peak=    3.322 closest distance to " CG1BVAL A  72 " =    1.761
peak=    3.322 closest distance to " O   HOH Z 415 " =    1.122
peak=    3.322 closest distance to " O   HOH Z  66 " =    2.087
peak=    3.321 closest distance to " O   HOH Z 294 " =    1.660
peak=    3.314 closest distance to " O   HOH Z 185 " =    1.745
peak=    3.314 closest distance to " C   VAL A 265 " =    1.178
peak=    3.314 closest distance to " O   HOH Z 417 " =    3.025
peak=    3.311 closest distance to " O  BHOH Z 338 " =    2.277
peak=    3.305 closest distance to " NZ  LYS A 117 " =    3.229
peak=    3.304 closest distance to " OE1 GLN A  58 " =    3.315
peak=    3.304 closest distance to " O   HOH Z 155 " =    1.331
peak=    3.303 closest distance to " O   HOH Z 281 " =    4.622
peak=    3.301 closest distance to " O   HOH Z 141 " =    1.680
peak=    3.298 closest distance to " NH2AARG A 190 " =    1.157
peak=    3.297 closest distance to " C   GLY A  80 " =    1.166
peak=    3.296 closest distance to " O   ASP A 124 " =    1.414
peak=    3.293 closest distance to " O   HOH Z  39 " =    1.265
peak=    3.292 closest distance to " O   HOH Z 214 " =    2.471
peak=    3.290 closest distance to " O   HOH Z 346 " =    1.661
peak=    3.289 closest distance to " CB  GLN A 103 " =    0.778
peak=    3.289 closest distance to " O   HOH Z 434 " =    3.032
peak=    3.288 closest distance to " CD  PRO A  54 " =    0.895
peak=    3.285 closest distance to " O   HOH Z  43 " =    1.365
peak=    3.285 closest distance to " O   HOH Z   6 " =    1.088
peak=    3.282 closest distance to " CA  ARG A  36 " =    1.105
peak=    3.282 closest distance to " O   HOH Z 327 " =    1.704
peak=    3.276 closest distance to " O   HOH Z 421 " =    1.909
peak=    3.270 closest distance to " CD2 LEU A 255 " =    1.416
peak=    3.270 closest distance to " O   HOH Z 316 " =    2.936
peak=    3.270 closest distance to " O   HOH Z 364 " =    2.105
peak=    3.268 closest distance to " O   HOH Z 358 " =    1.427
peak=    3.264 closest distance to " OG BSER A 210 " =    1.050
peak=    3.264 closest distance to " CB  GLU A 175 " =    1.331
peak=    3.261 closest distance to " O   ASN A  74 " =    1.571
peak=    3.261 closest distance to " CB  VAL A 265 " =    1.274
peak=    3.255 closest distance to " O   ARG A 275 " =    0.755
peak=    3.254 closest distance to " CH2 TRP A 274 " =    2.053
peak=    3.248 closest distance to " CE BMET A  47 " =    1.422
peak=    3.247 closest distance to " O   HOH Z 359 " =    2.028
peak=    3.239 closest distance to " N   ARG A 156 " =    1.464
peak=    3.239 closest distance to " O   HOH Z 343 " =    2.508
peak=    3.233 closest distance to " O   HOH Z 325 " =    3.896
peak=    3.231 closest distance to " CG2 VAL A 126 " =    0.912
peak=    3.231 closest distance to " O   HOH Z 327 " =    2.701
peak=    3.230 closest distance to " CB  GLN A  89 " =    1.171
peak=    3.229 closest distance to " O   HOH Z 423 " =    3.433
peak=    3.226 closest distance to " CB  PHE A  16 " =    1.136
peak=    3.226 closest distance to " O   HOH Z 301 " =    1.578
peak=    3.226 closest distance to " N   LYS A 166 " =    0.834
peak=    3.225 closest distance to " OG BSER A 164 " =    2.402
peak=    3.221 closest distance to " O   TRP A 274 " =    1.676
peak=    3.218 closest distance to " CD1 TRP A 266 " =    1.204
peak=    3.215 closest distance to " N   TYR A 116 " =    1.686
peak=    3.215 closest distance to " CA  ASN A 217 " =    1.355
peak=    3.213 closest distance to " O   HOH Z 150 " =    1.815
peak=    3.213 closest distance to " CB  ALA A 100 " =    1.476
peak=    3.213 closest distance to " NZ  LYS A 117 " =    2.240
peak=    3.213 closest distance to " CB  LEU A  83 " =    0.809
peak=    3.210 closest distance to " O   HOH Z 109 " =    2.811
peak=    3.208 closest distance to " CB  ALA A  51 " =    0.824
peak=    3.207 closest distance to " CA  ALA A 100 " =    2.135
peak=    3.201 closest distance to " NZ  LYS A 166 " =    3.082
peak=    3.196 closest distance to " CA  GLY A  98 " =    1.095
peak=    3.196 closest distance to " CA  ARG A  66 " =    1.041
peak=    3.194 closest distance to " N   CYS A 260 " =    0.820
peak=    3.189 closest distance to " CA  ALA A 158 " =    1.136
peak=    3.189 closest distance to " CD BLYS A 290 " =    1.029
peak=    3.189 closest distance to " O   HOH Z  50 " =    3.485
peak=    3.188 closest distance to " CA  VAL A 125 " =    1.222
peak=    3.186 closest distance to " CB  PRO A  90 " =    1.012
peak=    3.174 closest distance to " CB  ALA A 129 " =    0.822
peak=    3.174 closest distance to " O   HOH Z 345 " =    2.918
peak=    3.174 closest distance to " CB  PRO A  54 " =    1.193
peak=    3.168 closest distance to " NZ  LYS A  76 " =    0.856
peak=    3.168 closest distance to " O   HOH Z 104 " =    2.850
peak=    3.167 closest distance to " O   HOH Z 403 " =    1.470
peak=    3.163 closest distance to " O   HOH Z 189 " =    2.936
peak=    3.163 closest distance to " O   HOH Z 124 " =    1.860
peak=    3.162 closest distance to " CA  ALA A 291 " =    0.909
peak=    3.161 closest distance to " O   HOH Z 258 " =    2.104
peak=    3.161 closest distance to " O   HOH Z 173 " =    2.325
peak=    3.160 closest distance to " CE3 TRP A  85 " =    1.123
peak=    3.153 closest distance to " O   HOH Z 139 " =    4.396
peak=    3.153 closest distance to " CA  THR A 221 " =    1.605
peak=    3.152 closest distance to " O   HOH Z  19 " =    1.426
peak=    3.149 closest distance to " O   HOH Z   2 " =    1.722
peak=    3.149 closest distance to " O   HOH Z 272 " =    1.941
peak=    3.148 closest distance to " CB  TYR A 116 " =    1.377
peak=    3.142 closest distance to " O   HOH Z 414 " =    1.674
peak=    3.142 closest distance to " O   HOH Z 145 " =    2.110
peak=    3.140 closest distance to " CG2 VAL A 257 " =    0.867
peak=    3.139 closest distance to " CD  LYS A 119 " =    1.946
peak=    3.139 closest distance to " O   HOH Z 386 " =    2.177
peak=    3.138 closest distance to " ND1 HIS A  81 " =    1.492
peak=    3.129 closest distance to " N   TRP A 150 " =    1.036
peak=    3.127 closest distance to " O   HOH Z 299 " =    2.159
peak=    3.125 closest distance to " O   HOH Z  88 " =    2.777
peak=    3.114 closest distance to " CA  ASP A 132 " =    1.282
peak=    3.107 closest distance to " CA  CYS A 201 " =    1.795
peak=    3.102 closest distance to " O   SER A 276 " =    1.227
peak=    3.101 closest distance to " CG2 ILE A 120 " =    1.074
peak=    3.101 closest distance to " O   HOH Z 147 " =    1.707
peak=    3.099 closest distance to " CB  ALA A 137 " =    1.117
peak=    3.098 closest distance to " O   HOH Z 146 " =    1.269
peak=    3.089 closest distance to " CB  TRP A 179 " =    1.965
peak=    3.088 closest distance to " CB  ARG A  79 " =    0.828
peak=    3.086 closest distance to " O   HOH Z  48 " =    1.636
peak=    3.084 closest distance to " O   LYS A 290 " =    1.852
peak=    3.067 closest distance to " O   HOH Z 219 " =    4.957
peak=    3.065 closest distance to " O   HOH Z 404 " =    2.284
peak=    3.063 closest distance to " CA  ASP A 149 " =    1.308
peak=    3.059 closest distance to " CG  GLU A  37 " =    0.972
peak=    3.057 closest distance to " O   HOH Z 279 " =    2.146
peak=    3.054 closest distance to " CA  GLN A  11 " =    1.113
peak=    3.052 closest distance to " CB  LEU A 143 " =    1.151

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 224         
Filter by distance & map next to the model:
   mapped sites are within: 0.542 - 5.234
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 224
   mapped sites are within: 0.773 - 5.234

peak=   -4.435 closest distance to " O   HOH Z 266 " =    4.959
peak=   -4.287 closest distance to " NH2 ARG A  66 " =    1.382
peak=   -4.245 closest distance to " O   HOH Z 196 " =    1.729
peak=   -4.196 closest distance to " CB  LEU A 167 " =    2.167
peak=   -4.180 closest distance to " CA  SER A 164 " =    2.145
peak=   -4.177 closest distance to " CD  GLN A 223 " =    1.499
peak=   -4.160 closest distance to " CD1 PHE A  59 " =    1.984
peak=   -4.145 closest distance to " O   HOH Z 155 " =    1.517
peak=   -4.052 closest distance to " O   HOH Z 377 " =    0.868
peak=   -4.043 closest distance to " O   HOH Z 290 " =    0.910
peak=   -4.035 closest distance to " O   HOH Z 348 " =    2.394
peak=   -4.031 closest distance to " OXT GLY A 302 " =    2.987
peak=   -4.023 closest distance to " CG2 ILE A  49 " =    2.695
peak=   -3.992 closest distance to " CD  ARG A 156 " =    2.140
peak=   -3.992 closest distance to " C   ASN A 285 " =    2.355
peak=   -3.985 closest distance to " O   GLN A  11 " =    1.004
peak=   -3.985 closest distance to " CB  SER A 146 " =    2.203
peak=   -3.953 closest distance to " C   THR A 279 " =    1.069
peak=   -3.948 closest distance to " CD  GLN A  88 " =    0.912
peak=   -3.909 closest distance to " C   HIS A 108 " =    1.080
peak=   -3.903 closest distance to " CD  GLN A  58 " =    1.021
peak=   -3.883 closest distance to " O   PRO A 198 " =    1.337
peak=   -3.882 closest distance to " CA  VAL A 197 " =    0.969
peak=   -3.802 closest distance to " CE2 TYR A  30 " =    2.803
peak=   -3.791 closest distance to " CG  PRO A 243 " =    1.598
peak=   -3.778 closest distance to " O   HOH Z 407 " =    0.895
peak=   -3.772 closest distance to " ND2 ASN A  60 " =    1.397
peak=   -3.763 closest distance to " O   HOH Z  19 " =    2.305
peak=   -3.753 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.750 closest distance to " NH2 ARG A  66 " =    1.235
peak=   -3.745 closest distance to " OG  SER A  97 " =    2.230
peak=   -3.739 closest distance to " CD  GLN A 223 " =    0.954
peak=   -3.728 closest distance to " O   HOH Z   5 " =    1.657
peak=   -3.725 closest distance to " O   HOH Z  15 " =    1.613
peak=   -3.707 closest distance to " O   VAL A  67 " =    2.869
peak=   -3.686 closest distance to " O   HOH Z 185 " =    2.474
peak=   -3.680 closest distance to " CD  ARG A  14 " =    3.427
peak=   -3.664 closest distance to " O   HOH Z  71 " =    1.648
peak=   -3.662 closest distance to " N   ALA A  43 " =    2.687
peak=   -3.662 closest distance to " O   TRP A  92 " =    1.968
peak=   -3.648 closest distance to " OG  SER A  32 " =    0.970
peak=   -3.648 closest distance to " CA  GLU A 277 " =    1.260
peak=   -3.643 closest distance to " OH  TYR A 169 " =    0.905
peak=   -3.633 closest distance to " OD1 ASP A 191 " =    1.561
peak=   -3.632 closest distance to " CG  ASP A 231 " =    0.778
peak=   -3.627 closest distance to " O   HOH Z 308 " =    1.657
peak=   -3.597 closest distance to " OD2 ASP A 171 " =    1.910
peak=   -3.587 closest distance to " CD2 LEU A 237 " =    2.453
peak=   -3.586 closest distance to " O   HOH Z 418 " =    1.305
peak=   -3.583 closest distance to " CA  SER A 276 " =    1.419
peak=   -3.580 closest distance to " C   SER A 206 " =    1.411
peak=   -3.578 closest distance to " O   HOH Z 351 " =    1.483
peak=   -3.576 closest distance to " O   VAL A  67 " =    2.834
peak=   -3.574 closest distance to " O   HOH Z 392 " =    1.223
peak=   -3.572 closest distance to " O   HOH Z 151 " =    1.399
peak=   -3.572 closest distance to " CB  PRO A 243 " =    2.797
peak=   -3.568 closest distance to " O   HOH Z   7 " =    1.188
peak=   -3.566 closest distance to " O   PHE A 218 " =    1.377
peak=   -3.562 closest distance to " ND2 ASN A  45 " =    1.638
peak=   -3.559 closest distance to " O   HOH Z 109 " =    3.466
peak=   -3.552 closest distance to " O   HOH Z  58 " =    1.105
peak=   -3.550 closest distance to " O   HOH Z 120 " =    1.014
peak=   -3.547 closest distance to " CG  ARG A 269 " =    2.320
peak=   -3.544 closest distance to " O  BHOH Z 338 " =    1.283
peak=   -3.532 closest distance to " O   HOH Z  11 " =    1.330
peak=   -3.521 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.519 closest distance to " OE1 GLN A  88 " =    0.812
peak=   -3.512 closest distance to " O   HOH Z   6 " =    1.536
peak=   -3.506 closest distance to " O   HOH Z 222 " =    1.230
peak=   -3.501 closest distance to " CD2 PHE A  61 " =    1.978
peak=   -3.499 closest distance to " CD2 LEU A 300 " =    2.883
peak=   -3.495 closest distance to " CA  GLY A 203 " =    2.278
peak=   -3.489 closest distance to " O   HOH Z 423 " =    2.416
peak=   -3.488 closest distance to " O   HOH Z 207 " =    1.306
peak=   -3.481 closest distance to " O   ALA A   1 " =    2.093
peak=   -3.481 closest distance to " OG BSER A 210 " =    2.282
peak=   -3.480 closest distance to " ND2 ASN A  45 " =    1.017
peak=   -3.475 closest distance to " O   ALA A 256 " =    1.686
peak=   -3.472 closest distance to " CA  GLY A 241 " =    2.287
peak=   -3.472 closest distance to " O   HOH Z 221 " =    1.201
peak=   -3.468 closest distance to " O   SER A  95 " =    1.831
peak=   -3.466 closest distance to " O   HOH Z 243 " =    2.424
peak=   -3.461 closest distance to " O   ASP A 171 " =    1.068
peak=   -3.460 closest distance to " O   HOH Z 150 " =    1.836
peak=   -3.460 closest distance to " O   HOH Z 165 " =    1.974
peak=   -3.452 closest distance to " O   HOH Z 150 " =    1.013
peak=   -3.452 closest distance to " CD2 LEU A 237 " =    2.630
peak=   -3.449 closest distance to " CG2 THR A 182 " =    2.373
peak=   -3.448 closest distance to " O   HOH Z  93 " =    1.792
peak=   -3.439 closest distance to " O   HOH Z 388 " =    1.947
peak=   -3.439 closest distance to " N   SER A 134 " =    1.237
peak=   -3.433 closest distance to " O   HOH Z  52 " =    1.841
peak=   -3.428 closest distance to " O   ALA A  10 " =    1.714
peak=   -3.427 closest distance to " O   HOH Z  91 " =    2.399
peak=   -3.427 closest distance to " NH2BARG A 145 " =    2.243
peak=   -3.426 closest distance to " CB  ASP A 162 " =    2.571
peak=   -3.425 closest distance to " CB  ALA A  43 " =    2.641
peak=   -3.423 closest distance to " NH1 ARG A 195 " =    2.341
peak=   -3.422 closest distance to " N   ASP A 272 " =    1.231
peak=   -3.419 closest distance to " CD2 PHE A  59 " =    2.377
peak=   -3.417 closest distance to " CD  PRO A 213 " =    2.269
peak=   -3.416 closest distance to " O   HOH Z 109 " =    3.352
peak=   -3.413 closest distance to " O   HOH Z 171 " =    2.420
peak=   -3.409 closest distance to " O   ALA A  34 " =    2.451
peak=   -3.409 closest distance to " C   TRP A 274 " =    1.404
peak=   -3.408 closest distance to " O   HOH Z 422 " =    1.042
peak=   -3.406 closest distance to " O   HOH Z  37 " =    1.484
peak=   -3.403 closest distance to " CE  MET A  93 " =    1.906
peak=   -3.402 closest distance to " O   HOH Z 196 " =    2.520
peak=   -3.402 closest distance to " OG BSER A 210 " =    1.194
peak=   -3.401 closest distance to " O   HOH Z 234 " =    4.317
peak=   -3.395 closest distance to " CB  ALA A  10 " =    2.058
peak=   -3.391 closest distance to " N   GLN A  58 " =    1.421
peak=   -3.388 closest distance to " CG  MET A  93 " =    2.532
peak=   -3.387 closest distance to " O   HOH Z 136 " =    2.053
peak=   -3.382 closest distance to " CD  ARG A 195 " =    5.033
peak=   -3.378 closest distance to " O   HOH Z 196 " =    2.193
peak=   -3.366 closest distance to " O   HOH Z 422 " =    1.542
peak=   -3.365 closest distance to " OE1 GLN A  88 " =    1.134
peak=   -3.362 closest distance to " OG1 THR A  82 " =    1.414
peak=   -3.355 closest distance to " C   ALA A 158 " =    1.319
peak=   -3.354 closest distance to " O   HOH Z 275 " =    1.497
peak=   -3.349 closest distance to " OD1 ASN A 148 " =    1.500
peak=   -3.347 closest distance to " CA  PRO A 198 " =    1.122
peak=   -3.344 closest distance to " SD  MET A 105 " =    0.926
peak=   -3.341 closest distance to " CD1 TRP A 179 " =    0.907
peak=   -3.340 closest distance to " O   ALA A  34 " =    1.998
peak=   -3.339 closest distance to " ND2 ASN A  60 " =    1.759
peak=   -3.327 closest distance to " CB  ALA A 291 " =    2.494
peak=   -3.322 closest distance to " O   THR A  18 " =    1.618
peak=   -3.320 closest distance to " CH2 TRP A 179 " =    1.158
peak=   -3.314 closest distance to " OE1 GLN A 223 " =    2.392
peak=   -3.314 closest distance to " CG  ASP A  50 " =    2.357
peak=   -3.313 closest distance to " NH2 ARG A  79 " =    1.952
peak=   -3.312 closest distance to " O   ILE A 109 " =    2.603
peak=   -3.304 closest distance to " O   HOH Z 200 " =    1.241
peak=   -3.303 closest distance to " O   HOH Z  48 " =    0.920
peak=   -3.297 closest distance to " O   HOH Z 184 " =    1.382
peak=   -3.288 closest distance to " O   HOH Z 350 " =    1.055
peak=   -3.286 closest distance to " OG  SER A  87 " =    1.765
peak=   -3.285 closest distance to " OD2 ASP A 171 " =    2.285
peak=   -3.283 closest distance to " CG2AVAL A  41 " =    2.893
peak=   -3.283 closest distance to " CH2 TRP A 177 " =    1.949
peak=   -3.282 closest distance to " CE3 TRP A 150 " =    2.036
peak=   -3.282 closest distance to " OE2 GLU A   2 " =    1.450
peak=   -3.282 closest distance to " CB  PRO A 213 " =    1.745
peak=   -3.280 closest distance to " N   ALA A 226 " =    2.019
peak=   -3.279 closest distance to " CD1 PHE A 130 " =    2.357
peak=   -3.275 closest distance to " CD2 HIS A 115 " =    1.072
peak=   -3.272 closest distance to " O   GLY A 196 " =    1.111
peak=   -3.271 closest distance to " CD1 LEU A  25 " =    2.518
peak=   -3.269 closest distance to " CB  ALA A   9 " =    2.719
peak=   -3.263 closest distance to " O   HOH Z  49 " =    1.000
peak=   -3.259 closest distance to " O   HOH Z  35 " =    2.182
peak=   -3.258 closest distance to " O   HOH Z 313 " =    1.407
peak=   -3.254 closest distance to " O   HOH Z 292 " =    4.490
peak=   -3.251 closest distance to " O   HOH Z 298 " =    2.906
peak=   -3.251 closest distance to " CG2 THR A   4 " =    1.807
peak=   -3.246 closest distance to " O   HOH Z 119 " =    5.234
peak=   -3.244 closest distance to " O   HOH Z 426 " =    2.001
peak=   -3.244 closest distance to " NH2 ARG A  66 " =    4.183
peak=   -3.243 closest distance to " CD2 LEU A 167 " =    1.838
peak=   -3.242 closest distance to " N   GLY A 302 " =    1.901
peak=   -3.240 closest distance to " O   HOH Z 134 " =    1.928
peak=   -3.236 closest distance to " CG2 VAL A 189 " =    2.179
peak=   -3.234 closest distance to " C   ILE A 239 " =    2.229
peak=   -3.234 closest distance to " O   VAL A 174 " =    1.994
peak=   -3.232 closest distance to " CG  GLU A  53 " =    1.324
peak=   -3.228 closest distance to " NH2 ARG A  79 " =    1.876
peak=   -3.227 closest distance to " O   HOH Z 407 " =    1.656
peak=   -3.225 closest distance to " NE1 TRP A 177 " =    2.029
peak=   -3.225 closest distance to " O   HOH Z 403 " =    1.056
peak=   -3.225 closest distance to " CG2 ILE A 263 " =    2.300
peak=   -3.225 closest distance to " O   ARG A 275 " =    2.099
peak=   -3.222 closest distance to " OD1 ASP A 298 " =    2.059
peak=   -3.219 closest distance to " O   TYR A  15 " =    1.610
peak=   -3.218 closest distance to " O   HOH Z 251 " =    1.810
peak=   -3.216 closest distance to " O   HOH Z 368 " =    1.886
peak=   -3.213 closest distance to " CD1 ILE A 263 " =    2.047
peak=   -3.208 closest distance to " CD2 PHE A 225 " =    1.272
peak=   -3.206 closest distance to " NE2 GLN A  94 " =    1.690
peak=   -3.205 closest distance to " NH2 ARG A 159 " =    2.375
peak=   -3.202 closest distance to " NE2 GLN A 194 " =    1.889
peak=   -3.195 closest distance to " O   HOH Z  38 " =    1.366
peak=   -3.195 closest distance to " OD1 ASN A 301 " =    0.936
peak=   -3.192 closest distance to " O   SER A  26 " =    1.529
peak=   -3.191 closest distance to " O   HOH Z 369 " =    2.324
peak=   -3.191 closest distance to " N   GLY A  17 " =    1.715
peak=   -3.188 closest distance to " CB  SER A 210 " =    1.193
peak=   -3.187 closest distance to " OD1 ASN A 173 " =    1.550
peak=   -3.185 closest distance to " O   HOH Z 150 " =    1.982
peak=   -3.182 closest distance to " CG  ASP A 132 " =    2.425
peak=   -3.174 closest distance to " O   HOH Z 118 " =    5.084
peak=   -3.168 closest distance to " CG  GLN A  11 " =    1.440
peak=   -3.164 closest distance to " OG1 THR A  82 " =    1.288
peak=   -3.161 closest distance to " O   HOH Z   7 " =    1.574
peak=   -3.154 closest distance to " CG1 VAL A 197 " =    2.316
peak=   -3.154 closest distance to " CA  ASN A 127 " =    1.035
peak=   -3.152 closest distance to " O   HOH Z 423 " =    1.307
peak=   -3.149 closest distance to " ND2 ASN A  69 " =    1.432
peak=   -3.144 closest distance to " CG2BVAL A  41 " =    1.199
peak=   -3.138 closest distance to " CB  ALA A 100 " =    1.910
peak=   -3.136 closest distance to " O   HOH Z 111 " =    1.471
peak=   -3.135 closest distance to " O   ARG A  79 " =    0.976
peak=   -3.133 closest distance to " O   HOH Z 331 " =    1.201
peak=   -3.128 closest distance to " CZ  TYR A 169 " =    1.886
peak=   -3.122 closest distance to " NE1 TRP A 150 " =    2.173
peak=   -3.120 closest distance to " CG1 VAL A 112 " =    2.357
peak=   -3.112 closest distance to " CE  MET A 105 " =    1.993
peak=   -3.104 closest distance to " O   HOH Z 210 " =    1.183
peak=   -3.093 closest distance to " O   HOH Z 423 " =    1.527
peak=   -3.084 closest distance to " CE2 PHE A  61 " =    2.609
peak=   -3.082 closest distance to " SD  MET A  93 " =    1.595
peak=   -3.079 closest distance to " O   HOH Z 177 " =    1.925
peak=   -3.075 closest distance to " O   HOH Z  30 " =    0.773
peak=   -3.075 closest distance to " O   HOH Z 139 " =    3.390
peak=   -3.072 closest distance to " O   SER A   3 " =    1.154
peak=   -3.069 closest distance to " OG BSER A 216 " =    2.322
peak=   -3.049 closest distance to " O   HOH Z  25 " =    2.029
peak=   -3.039 closest distance to " O   HOH Z  40 " =    2.932
peak=   -3.030 closest distance to " O   HOH Z 146 " =    1.171
peak=   -3.008 closest distance to " CG  GLU A   2 " =    1.571

================= 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    :  0.4138 0.3957   6.233895e+00   6.190975e+00
   1_bss:  0.3994 0.3809   6.218893e+00   6.172411e+00
   1_xyz:  0.3330 0.3613   6.079027e+00   6.127237e+00
   1_adp:  0.3087 0.3687   6.034259e+00   6.137630e+00
   1_occ:  0.3084 0.3682   6.033529e+00   6.137368e+00
   2_bss:  0.3073 0.3663   6.035111e+00   6.137903e+00
   2_xyz:  0.2536 0.3036   5.852553e+00   5.990920e+00
   2_adp:  0.2379 0.2991   5.819532e+00   5.979252e+00
   2_occ:  0.2377 0.2990   5.819123e+00   5.979190e+00
   3_bss:  0.2376 0.2978   5.818334e+00   5.978063e+00
   3_xyz:  0.1863 0.2381   5.587638e+00   5.778066e+00
   3_adp:  0.1704 0.2206   5.510832e+00   5.710768e+00
   3_occ:  0.1703 0.2205   5.510266e+00   5.710413e+00
   4_bss:  0.1701 0.2203   5.509907e+00   5.708732e+00
   4_xyz:  0.1427 0.1879   5.349304e+00   5.560292e+00
   4_adp:  0.1344 0.1814   5.300507e+00   5.519910e+00
   4_occ:  0.1343 0.1814   5.300114e+00   5.519705e+00
   5_bss:  0.1345 0.1818   5.301602e+00   5.520781e+00
   5_xyz:  0.1274 0.1750   5.258451e+00   5.487465e+00
   5_adp:  0.1271 0.1717   5.249045e+00   5.468696e+00
   5_occ:  0.1270 0.1715   5.248243e+00   5.468040e+00
   5_bss:  0.1270 0.1715   5.248139e+00   5.467941e+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:  0.290  27.820  -3.210   6.070  -1.824   0.000  -0.000  -0.000
   1_xyz:  0.290  27.820  -3.210   6.070  -1.824   0.000  -0.000  -0.000
   1_adp:  0.290  27.820  -3.210   6.070  -1.824   0.000  -0.000  -0.000
   1_occ:  0.290  27.820  -3.210   6.070  -1.824   0.000  -0.000  -0.000
   2_bss:  0.297  42.298  -1.836   3.445  -0.672   0.000  -0.000  -0.000
   2_xyz:  0.297  42.298  -1.836   3.445  -0.672   0.000  -0.000  -0.000
   2_adp:  0.297  42.298  -1.836   3.445  -0.672   0.000  -0.000  -0.000
   2_occ:  0.297  42.298  -1.836   3.445  -0.672   0.000  -0.000  -0.000
   3_bss:  0.312  58.910  -1.240   2.022  -0.205   0.000  -0.000  -0.000
   3_xyz:  0.312  58.910  -1.240   2.022  -0.205   0.000  -0.000  -0.000
   3_adp:  0.312  58.910  -1.240   2.022  -0.205   0.000  -0.000  -0.000
   3_occ:  0.312  58.910  -1.240   2.022  -0.205   0.000  -0.000  -0.000
   4_bss:  0.326  70.094  -1.419   0.597  -0.406   0.000  -0.000  -0.000
   4_xyz:  0.326  70.094  -1.419   0.597  -0.406   0.000  -0.000  -0.000
   4_adp:  0.326  70.094  -1.419   0.597  -0.406   0.000  -0.000  -0.000
   4_occ:  0.326  70.094  -1.419   0.597  -0.406   0.000  -0.000  -0.000
   5_bss:  0.328  69.023  -1.412   0.019  -0.290   0.000  -0.000  -0.000
   5_xyz:  0.328  69.023  -1.412   0.019  -0.290   0.000  -0.000  -0.000
   5_adp:  0.328  69.023  -1.412   0.019  -0.290   0.000  -0.000  -0.000
   5_occ:  0.328  69.023  -1.412   0.019  -0.290   0.000  -0.000  -0.000
   5_bss:  0.324  65.472  -1.395  -0.207  -0.244  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.705 0.6015  0.7731    49381.386
   1_bss:  42.800 0.6110  0.7878    45657.287
   1_xyz:  40.921 0.6318  0.8061    39545.590
   1_adp:  41.562 0.6237  0.7865    40417.576
   1_occ:  41.573 0.6235  0.7854    40359.682
   2_bss:  41.227 0.6279  0.7954    40151.825
   2_xyz:  32.548 0.7285  0.9034    25424.679
   2_adp:  31.724 0.7382  0.8967    24604.562
   2_occ:  31.726 0.7381  0.8964    24595.936
   3_bss:  31.512 0.7406  0.8972    24344.240
   3_xyz:  24.083 0.8203  0.9660    14784.610
   3_adp:  21.783 0.8443  0.9691    12797.568
   3_occ:  21.765 0.8445  0.9693    12794.038
   4_bss:  21.646 0.8456  0.9511    12685.167
   4_xyz:  17.988 0.8801  0.9701     9002.000
   4_adp:  16.932 0.8901  0.9669     8334.987
   4_occ:  16.922 0.8902  0.9668     8332.456
   5_bss:  16.937 0.8901  0.9621     8362.738
   5_xyz:  16.158 0.8970  0.9664     7787.652
   5_adp:  15.719 0.9010  0.9628     7561.937
   5_occ:  15.701 0.9012  0.9630     7551.128
   5_bss:  15.699 0.9012  0.9606     7547.011
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6916e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6916e-01
   1_xyz:   1.423  0.011  0.087 15.949  0.006  4.113   1.0571e-01
   1_adp:   1.423  0.011  0.087 15.949  0.006  4.113   1.0571e-01
   1_occ:   1.423  0.011  0.087 15.949  0.006  4.113   1.0571e-01
   2_bss:   1.423  0.011  0.087 15.949  0.006  4.113   1.0571e-01
   2_xyz:   1.293  0.009  0.082 14.889  0.006  4.114   8.7652e-02
   2_adp:   1.293  0.009  0.082 14.889  0.006  4.114   8.7652e-02
   2_occ:   1.293  0.009  0.082 14.889  0.006  4.114   8.7652e-02
   3_bss:   1.293  0.009  0.082 14.889  0.006  4.114   8.7652e-02
   3_xyz:   1.159  0.010  0.077 15.032  0.005  4.127   7.8378e-02
   3_adp:   1.159  0.010  0.077 15.032  0.005  4.127   7.8378e-02
   3_occ:   1.159  0.010  0.077 15.032  0.005  4.127   7.8378e-02
   4_bss:   1.159  0.010  0.077 15.032  0.005  4.127   7.8378e-02
   4_xyz:   1.075  0.008  0.076 14.658  0.004  4.124   6.6314e-02
   4_adp:   1.075  0.008  0.076 14.658  0.004  4.124   6.6314e-02
   4_occ:   1.075  0.008  0.076 14.658  0.004  4.124   6.6314e-02
   5_bss:   1.075  0.008  0.076 14.658  0.004  4.124   6.6314e-02
   5_xyz:   0.950  0.007  0.070 14.552  0.004  4.128   5.4499e-02
   5_adp:   0.950  0.007  0.070 14.552  0.004  4.128   5.4499e-02
   5_occ:   0.950  0.007  0.070 14.552  0.004  4.128   5.4499e-02
   5_bss:   0.950  0.007  0.070 14.552  0.004  4.128   5.4499e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.599   2.4337e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.599   2.4337e-01
   1_xyz:   9.015  0.058  0.417 84.704  0.044  2.165   9.9135e-02
   1_adp:   9.015  0.058  0.417 84.704  0.044  2.165   9.9135e-02
   1_occ:   9.015  0.058  0.417 84.704  0.044  2.165   9.9135e-02
   2_bss:   9.015  0.058  0.417 84.704  0.044  2.165   9.9135e-02
   2_xyz:   8.210  0.042  0.296 83.160  0.075  2.226   9.0749e-02
   2_adp:   8.210  0.042  0.296 83.160  0.075  2.226   9.0749e-02
   2_occ:   8.210  0.042  0.296 83.160  0.075  2.226   9.0749e-02
   3_bss:   8.210  0.042  0.296 83.160  0.075  2.226   9.0749e-02
   3_xyz:   7.627  0.054  0.238 86.647  0.041  2.207   6.4105e-02
   3_adp:   7.627  0.054  0.238 86.647  0.041  2.207   6.4105e-02
   3_occ:   7.627  0.054  0.238 86.647  0.041  2.207   6.4105e-02
   4_bss:   7.627  0.054  0.238 86.647  0.041  2.207   6.4105e-02
   4_xyz:   7.538  0.060  0.251 82.981  0.041  2.265   6.1181e-02
   4_adp:   7.538  0.060  0.251 82.981  0.041  2.265   6.1181e-02
   4_occ:   7.538  0.060  0.251 82.981  0.041  2.265   6.1181e-02
   5_bss:   7.538  0.060  0.251 82.981  0.041  2.265   6.1181e-02
   5_xyz:   7.142  0.033  0.230 82.029  0.035  2.412   3.5816e-02
   5_adp:   7.142  0.033  0.230 82.029  0.035  2.412   3.5816e-02
   5_occ:   7.142  0.033  0.230 82.029  0.035  2.412   3.5816e-02
   5_bss:   7.142  0.033  0.230 82.029  0.035  2.412   3.5816e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  85.41   0.00  17.34  80.97   0.00  14.23  85.41   2.15  34.27
   1_occ:  85.41   0.00  17.34  80.97   0.00  14.23  85.41   2.15  34.27
   2_bss:  85.41   0.00  17.34  80.97   0.00  14.23  85.41   2.15  34.27
   2_xyz:  85.41   0.00  17.34  80.97   0.00  14.23  85.41   2.15  34.27
   2_adp:  89.67   0.00  17.62  89.67   0.00  13.98  86.25   0.89  37.47
   2_occ:  89.67   0.00  17.62  89.67   0.00  13.98  86.25   0.89  37.47
   3_bss:  89.67   0.00  17.62  89.67   0.00  13.98  86.25   0.89  37.47
   3_xyz:  89.67   0.00  17.62  89.67   0.00  13.98  86.25   0.89  37.47
   3_adp:  93.57   0.00  17.27  93.57   0.00  12.90  89.70   4.33  41.08
   3_occ:  93.57   0.00  17.27  93.57   0.00  12.90  89.70   4.33  41.08
   4_bss:  93.57   0.00  17.27  93.57   0.00  12.90  89.70   4.33  41.08
   4_xyz:  93.57   0.00  17.27  93.57   0.00  12.90  89.70   4.33  41.08
   4_adp: 103.92   0.39  17.02 103.92   0.39  12.27 100.38   1.91  42.86
   4_occ: 103.92   0.39  17.02 103.92   0.39  12.27 100.38   1.91  42.86
   5_bss: 103.92   0.39  17.02 103.92   0.39  12.27 100.38   1.91  42.86
   5_xyz: 103.92   0.39  17.02 103.92   0.39  12.27 100.38   1.91  42.86
   5_adp: 100.41   0.72  16.45 100.41   0.72  11.93  99.28   3.91  41.02
   5_occ: 100.41   0.72  16.45 100.41   0.72  11.93  99.28   3.91  41.02
   5_bss: 100.39   0.70  16.42 100.39   0.70  11.91  99.26   3.88  41.00
------------------------------------------------------------------------
 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:    1.580    0.007    0.288
   1_adp:    1.580    0.007    0.288
   1_occ:    1.580    0.007    0.288
   2_bss:    1.580    0.007    0.288
   2_xyz:    1.407    0.036    0.474
   2_adp:    1.407    0.036    0.474
   2_occ:    1.407    0.036    0.474
   3_bss:    1.407    0.036    0.474
   3_xyz:    1.494    0.054    0.641
   3_adp:    1.494    0.054    0.641
   3_occ:    1.494    0.054    0.641
   4_bss:    1.494    0.054    0.641
   4_xyz:    1.635    0.071    0.712
   4_adp:    1.635    0.071    0.712
   4_occ:    1.635    0.071    0.712
   5_bss:    1.635    0.071    0.712
   5_xyz:    1.592    0.053    0.738
   5_adp:    1.592    0.053    0.738
   5_occ:    1.592    0.053    0.738
   5_bss:    1.592    0.053    0.738
------------------------------------------------------------------------

CPU time actual refinement: 278.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/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_840/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_840/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 277.99 
  Macro-tasks:
    bulk solvent and scale       = 31.67  
    individual site refinement   = 115.80 
    weights calculation          = 24.43  
    collect and process          = 5.36   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 177.34 
  Micro-tasks:
    mask                            = 2.03   
    f_calc                          = 89.39  
    alpha_beta                      = 7.15   
    target                          = 1.03   
    gradients_wrt_atomic_parameters = 97.17  
    fmodel                         = 5.31   
    r_factors                      = 0.11   
    phase_errors                   = 8.84   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 211.25 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.950 micro seconds
Total CPU time: 4.83 minutes
from_scatterers_fft:    643 calls, 89.06 s
gradients_fft:          588 calls, 85.82 s

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

# Date 2008-01-16 Time 05:46:37 PST -0800 (1200491197.77 s)
Start R-work = 0.4138, R-free = 0.3957 (no bulk solvent and anisotropic scale)
Final R-work = 0.1439, R-free = 0.1870 (no bulk solvent and anisotropic scale)

Start R-work = 0.3994, R-free = 0.3809
Final R-work = 0.1270, R-free = 0.1715