# Date 2008-01-16 Time 06:10:56 PST -0800 (1200492656.04 s)
#phil __OFF__

Command line arguments: "../1036.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11409
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1036

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97125
Completeness in resolution range: 0.940648
Completeness with d_max=infinity: 0.937811

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9712

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: (71.3037, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97125
Completeness in resolution range: 0.940648
Completeness with d_max=infinity: 0.937811

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2189 [2188/2217]  1972   216   9.9%
  bin  2:  4.2189 -  3.3608 [2095/2114]  1884   211  10.1%
  bin  3:  3.3608 -  2.9396 [2073/2093]  1862   211  10.2%
  bin  4:  2.9396 -  2.6724 [2059/2084]  1862   197   9.6%
  bin  5:  2.6724 -  2.4818 [2049/2068]  1836   213  10.4%
  bin  6:  2.4818 -  2.3360 [2027/2073]  1829   198   9.8%
  bin  7:  2.3360 -  2.2194 [2014/2047]  1813   201  10.0%
  bin  8:  2.2194 -  2.1231 [2012/2048]  1810   202  10.0%
  bin  9:  2.1231 -  2.0415 [2010/2039]  1807   203  10.1%
  bin 10:  2.0415 -  1.9712 [1062/2042]   955   107  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2187
        3.04 -     3.66: 4675
        3.66 -     4.28: 8990
        4.28 -     4.90: 12373
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.921 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.947 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.091 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28248 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_1036/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 = 71.30375 47.16465 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3534   r_free= 0.3591   ksol= 0.00   Bsol= 0.00   scale= 0.957    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.101418                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.2912 0.2913      6.3693      6.3441|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.2708 0.2650      6.4781      6.4454|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.3065 0.2950      6.3809      6.4625|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.3288 0.3397      6.2748      6.2653|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.3528 0.3575      6.1456      6.2137|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.3931 0.3907      6.1065      6.0366|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.3802 0.3431       6.087       6.014|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.3952 0.4068        6.01      6.0846|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.4033 0.4102      5.9875      5.9421|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.4091 0.4757      5.9693      6.0676|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.4173 0.4882      5.9209      5.9993|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.4231 0.4511      5.8582      5.9179|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.4195 0.4098      5.7817      5.7214|
| 14:  2.0204 -  1.9712 0.36    476   51 0.4635 0.4460       5.766      5.7244|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.79  25.65   0.86     0.80      42076.89|
|  2:  4.7060 -  3.7542  1370   144  0.82  24.10   0.97     0.90      50988.28|
|  3:  3.7542 -  3.2852  1336   158  0.77  29.13   0.97     0.92      53440.48|
|  4:  3.2852 -  2.9874  1344   148  0.72  33.37   0.99     0.90      49461.27|
|  5:  2.9874 -  2.7747  1311   147  0.66  38.75   0.97     0.85      42136.80|
|  6:  2.7747 -  2.6120  1320   146  0.65  39.92   0.98     0.84      36285.45|
|  7:  2.6120 -  2.4818  1318   146  0.67  38.07   0.98     0.85      32005.24|
|  8:  2.4818 -  2.3742  1293   139  0.65  40.30   0.97     0.87      30995.48|
|  9:  2.3742 -  2.2831  1318   153  0.62  42.65   1.01     0.85      30276.09|
| 10:  2.2831 -  2.2046  1283   139  0.58  45.71   1.01     0.81      32558.98|
| 11:  2.2046 -  2.1358  1299   144  0.55  48.12   1.02     0.78      31222.05|
| 12:  2.1358 -  2.0749  1282   144  0.54  49.13   1.00     0.80      29737.26|
| 13:  2.0749 -  2.0204  1263   141  0.55  48.44   1.00     0.79      24222.86|
| 14:  2.0204 -  1.9712   476    51  0.54  49.03   0.98     0.74      19914.41|
|alpha:            min =        0.74 max =            0.92 mean =         0.84|
|beta:             min =    19914.41 max =        53440.48 mean =     37049.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.94 mean =        38.78|
|phase err.(test): min =        0.00 max =           89.97 mean =        38.82|
|-----------------------------------------------------------------------------|

============================== 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 = 5.411331              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.126   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      182 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2823 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4646 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4344 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5659 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6714 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.211 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    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: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3534   r_free= 0.3591   ksol= 0.00   Bsol= 0.00   scale= 0.957    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.101418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3423   r_free= 0.3482   ksol= 0.32   Bsol= 41.55   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,-1.90,0.86,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.087282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.545793              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.371   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.473846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.079   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3423      final r-factor (work) = 0.1947          |
| start r-factor (free) = 0.3482      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0032 = 4.55 * 0.50 * 6.0884 + 1.00 * 0.1649                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3262 = 4.55 * 0.50 * 5.8285 + 1.00 * 0.0786                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1947      final r-factor (work) = 0.1777          |
| start r-factor (free) = 0.2197      final r-factor (free) = 0.2239          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7681 = 0.47 * 1.00 * 5.8285 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6276 = 0.47 * 1.00 * 5.5249 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.90   17.34    None  None   None       |
|    all(noH): 2823   0      0.00    76.90   17.34    None  None   None       |
|    Sol.    : 438    0      6.64    76.90   39.98    None  None   None       |
|    Mac.    : 2385   0      0.00    74.59   13.19    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:     0.000 -   7.690:  488   |   5:    38.449 -  46.139:  110        |
|      1:     7.690 -  15.380: 1330   |   6:    46.139 -  53.829:  105        |
|      2:    15.380 -  23.069:  445   |   7:    53.829 -  61.518:   53        |
|      3:    23.069 -  30.759:  139   |   8:    61.518 -  69.208:   25        |
|      4:    30.759 -  38.449:  117   |   9:    69.208 -  76.898:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1777 r_free = 0.2239             target_work(ml) = 5.532         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1773 r_free = 0.2244             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1773   r_free= 0.2244   ksol= 0.32   Bsol= 41.55   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,-1.90,0.86,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.531165                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1753   r_free= 0.2218   ksol= 0.33   Bsol= 54.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.55,-1.36,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.527128                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.345561              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.750   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214179              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.113  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1753      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.2218      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3526 = 3.35 * 0.50 * 5.5440 + 1.00 * 0.0786                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1131 = 3.35 * 0.50 * 5.4110 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1686 = 0.21 * 1.00 * 5.4110 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1324 = 0.21 * 1.00 * 5.2509 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.44    76.97   17.10    None  None   None       |
|    all(noH): 2823   0      2.44    76.97   17.10    None  None   None       |
|    Sol.    : 438    0      5.56    76.55   39.11    None  None   None       |
|    Mac.    : 2385   0      2.44    76.97   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.437 -   9.891:  931   |   5:    39.706 -  47.160:  111        |
|      1:     9.891 -  17.345: 1102   |   6:    47.160 -  54.613:   92        |
|      2:    17.345 -  24.798:  284   |   7:    54.613 -  62.067:   41        |
|      3:    24.798 -  32.252:  125   |   8:    62.067 -  69.521:   27        |
|      4:    32.252 -  39.706:  105   |   9:    69.521 -  76.975:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1650             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1647             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1647   ksol= 0.33   Bsol= 54.72   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.55,-1.36,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.224037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1650   ksol= 0.33   Bsol= 54.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.54,-1.79,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225649                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.048500              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.333129              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.408  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0670 = 3.05 * 0.50 * 5.2520 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9688 = 3.05 * 0.50 * 5.1819 + 1.00 * 0.0703                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7340 = 0.33 * 1.00 * 5.1819 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7202 = 0.33 * 1.00 * 5.1394 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    80.64   17.06    None  None   None       |
|    all(noH): 2823   0      1.73    80.64   17.06    None  None   None       |
|    Sol.    : 438    0      5.97    76.23   39.10    None  None   None       |
|    Mac.    : 2385   0      1.73    80.64   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.730 -   9.621:  898   |   5:    41.183 -  49.073:  108        |
|      1:     9.621 -  17.511: 1150   |   6:    49.073 -  56.964:   83        |
|      2:    17.511 -  25.402:  289   |   7:    56.964 -  64.854:   42        |
|      3:    25.402 -  33.292:  123   |   8:    64.854 -  72.745:   16        |
|      4:    33.292 -  41.183:  108   |   9:    72.745 -  80.635:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1556             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1555             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1555   ksol= 0.33   Bsol= 54.72   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.54,-1.79,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1555   ksol= 0.33   Bsol= 54.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.40,-1.85,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137500                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.047635              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.814  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.336627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.056  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9015 = 3.05 * 0.50 * 5.1392 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8862 = 3.05 * 0.50 * 5.1279 + 1.00 * 0.0722                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7342 = 0.34 * 1.00 * 5.1279 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7337 = 0.34 * 1.00 * 5.1259 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    81.38   16.91    None  None   None       |
|    all(noH): 2823   0      1.69    81.38   16.91    None  None   None       |
|    Sol.    : 438    0      6.48    76.07   38.84    None  None   None       |
|    Mac.    : 2385   0      1.69    81.38   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.686 -   9.656:  926   |   5:    41.534 -  49.503:  111        |
|      1:     9.656 -  17.625: 1139   |   6:    49.503 -  57.473:   75        |
|      2:    17.625 -  25.595:  274   |   7:    57.473 -  65.442:   42        |
|      3:    25.595 -  33.564:  128   |   8:    65.442 -  73.411:   12        |
|      4:    33.564 -  41.534:  110   |   9:    73.411 -  81.381:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1565             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1565             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1565   ksol= 0.33   Bsol= 54.72   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.40,-1.85,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128066                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1565   ksol= 0.33   Bsol= 54.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.25,-1.73,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128130                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.352891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.085  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.333897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.015  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1072      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1030 = 2.35 * 0.50 * 5.1263 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1030 = 2.35 * 0.50 * 5.1325 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7219 = 0.33 * 1.00 * 5.1325 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7229 = 0.33 * 1.00 * 5.1355 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    83.58   16.75    None  None   None       |
|    all(noH): 2823   0      1.35    83.58   16.75    None  None   None       |
|    Sol.    : 438    0      6.35    75.70   38.41    None  None   None       |
|    Mac.    : 2385   0      1.35    83.58   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.351 -   9.575:  937   |   5:    42.468 -  50.691:  102        |
|      1:     9.575 -  17.798: 1149   |   6:    50.691 -  58.914:   67        |
|      2:    17.798 -  26.021:  265   |   7:    58.914 -  67.138:   33        |
|      3:    26.021 -  34.244:  131   |   8:    67.138 -  75.361:    9        |
|      4:    34.244 -  42.468:  124   |   9:    75.361 -  83.584:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1574             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1574             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1574   ksol= 0.33   Bsol= 54.72   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.25,-1.73,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136919                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.0979 0.1280      5.3749      5.5358|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.0839 0.1079      5.4184      5.6141|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.1039 0.1596      5.4574      5.8879|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.1190 0.1529      5.4471      5.5644|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.1276 0.1732      5.3136      5.5272|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.1215 0.1879      5.2043      5.4406|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.1176 0.1649      5.1344      5.3714|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.1076 0.1699      5.0167      5.2767|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.1125 0.1811      4.9979      5.3005|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.1102 0.1706       4.954      5.2114|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.1110 0.1843      4.9387      5.3064|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.1067 0.1614      4.8637      5.0816|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.1132 0.1713      4.7783      5.0322|
| 14:  2.0204 -  1.9712 0.36    476   51 0.0966 0.1667      4.6095       4.887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.94   8.50   0.98     0.95       6701.60|
|  2:  4.7060 -  3.7542  1370   144  0.95   7.88   1.01     1.00       8695.87|
|  3:  3.7542 -  3.2852  1336   158  0.93  11.47   1.02     1.01      10323.43|
|  4:  3.2852 -  2.9874  1344   148  0.92  13.96   1.00     0.98      10572.98|
|  5:  2.9874 -  2.7747  1311   147  0.90  16.38   0.99     0.96       8470.47|
|  6:  2.7747 -  2.6120  1320   146  0.90  16.30   0.98     0.95       7101.62|
|  7:  2.6120 -  2.4818  1318   146  0.91  14.88   0.99     0.96       5964.46|
|  8:  2.4818 -  2.3742  1293   139  0.91  14.96   0.99     0.97       5034.90|
|  9:  2.3742 -  2.2831  1318   153  0.91  15.41   0.99     0.96       4768.71|
| 10:  2.2831 -  2.2046  1283   139  0.91  15.23   0.98     0.95       4377.14|
| 11:  2.2046 -  2.1358  1299   144  0.89  16.79   0.99     0.96       4531.95|
| 12:  2.1358 -  2.0749  1282   144  0.91  15.35   0.99     0.98       4004.95|
| 13:  2.0749 -  2.0204  1263   141  0.90  16.17   0.99     0.98       3317.23|
| 14:  2.0204 -  1.9712   476    51  0.91  15.22   0.97     0.94       2432.89|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2432.89 max =        10572.98 mean =      6382.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1574   ksol= 0.33   Bsol= 54.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.07,-1.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1574   ksol= 0.33   Bsol= 54.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.07,-1.57,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136978                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7060 0.99   1417  159 0.0979 0.1281      5.3754      5.5365|
|  2:  4.7060 -  3.7542 0.99   1370  144 0.0839 0.1079      5.4185      5.6138|
|  3:  3.7542 -  3.2852 0.99   1336  158 0.1039 0.1596      5.4572      5.8876|
|  4:  3.2852 -  2.9874 0.99   1344  148 0.1190 0.1529       5.447      5.5646|
|  5:  2.9874 -  2.7747 0.99   1311  147 0.1276 0.1732      5.3137      5.5272|
|  6:  2.7747 -  2.6120 0.98   1320  146 0.1215 0.1878      5.2044      5.4406|
|  7:  2.6120 -  2.4818 0.99   1318  146 0.1176 0.1649      5.1344      5.3714|
|  8:  2.4818 -  2.3742 0.98   1293  139 0.1076 0.1699      5.0167      5.2766|
|  9:  2.3742 -  2.2831 0.98   1318  153 0.1125 0.1811       4.998      5.3004|
| 10:  2.2831 -  2.2046 0.98   1283  139 0.1102 0.1706       4.954      5.2113|
| 11:  2.2046 -  2.1358 0.99   1299  144 0.1110 0.1844      4.9388      5.3067|
| 12:  2.1358 -  2.0749 0.98   1282  144 0.1067 0.1614      4.8637      5.0816|
| 13:  2.0749 -  2.0204 0.95   1263  141 0.1132 0.1713      4.7782       5.032|
| 14:  2.0204 -  1.9712 0.36    476   51 0.0966 0.1669      4.6098      4.8875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7060  1417   159  0.94   8.50   0.98     0.95       6707.79|
|  2:  4.7060 -  3.7542  1370   144  0.95   7.88   1.01     1.00       8698.28|
|  3:  3.7542 -  3.2852  1336   158  0.93  11.47   1.02     1.01      10318.60|
|  4:  3.2852 -  2.9874  1344   148  0.92  13.96   1.00     0.98      10572.76|
|  5:  2.9874 -  2.7747  1311   147  0.90  16.38   0.99     0.97       8470.77|
|  6:  2.7747 -  2.6120  1320   146  0.90  16.30   0.98     0.96       7102.63|
|  7:  2.6120 -  2.4818  1318   146  0.91  14.88   0.99     0.97       5964.15|
|  8:  2.4818 -  2.3742  1293   139  0.91  14.96   0.99     0.97       5034.49|
|  9:  2.3742 -  2.2831  1318   153  0.91  15.41   1.00     0.97       4767.37|
| 10:  2.2831 -  2.2046  1283   139  0.91  15.23   0.99     0.95       4377.07|
| 11:  2.2046 -  2.1358  1299   144  0.89  16.80   1.00     0.96       4531.39|
| 12:  2.1358 -  2.0749  1282   144  0.91  15.36   1.00     0.99       4005.49|
| 13:  2.0749 -  2.0204  1263   141  0.90  16.17   1.00     0.99       3317.58|
| 14:  2.0204 -  1.9712   476    51  0.91  15.23   0.98     0.95       2433.99|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2433.99 max =        10572.76 mean =      6383.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.85 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.989)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    83.54   16.70    None  None   None       |
|    all(noH): 2823   0      1.30    83.54   16.70    None  None   None       |
|    Sol.    : 438    0      6.30    75.65   38.37    None  None   None       |
|    Mac.    : 2385   0      1.30    83.54   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.304 -   9.527:  937   |   5:    42.420 -  50.643:  102        |
|      1:     9.527 -  17.750: 1149   |   6:    50.643 -  58.867:   67        |
|      2:    17.750 -  25.973:  265   |   7:    58.867 -  67.090:   33        |
|      3:    25.973 -  34.197:  131   |   8:    67.090 -  75.313:    9        |
|      4:    34.197 -  42.420:  124   |   9:    75.313 -  83.536:    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)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.519 - 4.516
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 291
   mapped sites are within: 0.731 - 4.516

peak=    6.071 closest distance to " NH2 ARG A  56 " =    2.255
peak=    5.837 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.190 closest distance to " CB  SER A  63 " =    1.231
peak=    5.101 closest distance to " O   HOH Z 126 " =    1.872
peak=    4.934 closest distance to " O   HOH Z 232 " =    2.292
peak=    4.821 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.739 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.729 closest distance to " CG  PRO A 213 " =    1.194
peak=    4.588 closest distance to " OD1 ASN A  69 " =    2.577
peak=    4.550 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.535 closest distance to " CB  GLU A 128 " =    1.062
peak=    4.516 closest distance to " C   PRO A 198 " =    1.544
peak=    4.490 closest distance to " O   HOH Z 236 " =    1.991
peak=    4.470 closest distance to " O   HOH Z 193 " =    1.956
peak=    4.458 closest distance to " O   HOH Z 298 " =    1.893
peak=    4.431 closest distance to " CB  GLU A 152 " =    1.164
peak=    4.406 closest distance to " O   HOH Z  78 " =    1.659
peak=    4.391 closest distance to " NE2 GLN A  11 " =    1.087
peak=    4.337 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.331 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.290 closest distance to " CG  PRO A  90 " =    1.103
peak=    4.234 closest distance to " CG  PRO A 198 " =    1.329
peak=    4.210 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.190 closest distance to " CA  ALA A  21 " =    1.228
peak=    4.181 closest distance to " O   HOH Z 369 " =    1.986
peak=    4.176 closest distance to " CB  ASN A 148 " =    1.442
peak=    4.174 closest distance to " OD2 ASP A 286 " =    2.888
peak=    4.167 closest distance to " O   HOH Z  15 " =    2.131
peak=    4.158 closest distance to " O   HOH Z 368 " =    2.055
peak=    4.150 closest distance to " O   HOH Z 427 " =    2.968
peak=    4.130 closest distance to " O   HOH Z 142 " =    1.623
peak=    4.104 closest distance to " CB  SER A   3 " =    1.375
peak=    4.093 closest distance to " NH2 ARG A 156 " =    1.207
peak=    4.091 closest distance to " ND2 ASN A 187 " =    1.516
peak=    4.035 closest distance to " CB  ARG A  79 " =    1.404
peak=    4.023 closest distance to " O   HOH Z 303 " =    2.016
peak=    4.021 closest distance to " CA  THR A 221 " =    1.005
peak=    4.001 closest distance to " O   HOH Z 132 " =    2.618
peak=    4.000 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.994 closest distance to " O   HOH Z 403 " =    1.682
peak=    3.984 closest distance to " O   HOH Z 234 " =    3.771
peak=    3.970 closest distance to " O   HOH Z 261 " =    2.269
peak=    3.970 closest distance to " CD1 LEU A 300 " =    1.247
peak=    3.937 closest distance to " CB  ASN A 187 " =    1.109
peak=    3.921 closest distance to " CZ  PHE A 218 " =    1.064
peak=    3.913 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.898 closest distance to " O   HOH Z 108 " =    2.204
peak=    3.885 closest distance to " NH2BARG A 145 " =    2.139
peak=    3.879 closest distance to " O   HOH Z 214 " =    2.015
peak=    3.873 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.872 closest distance to " O   HOH Z 135 " =    1.696
peak=    3.867 closest distance to " ND2 ASN A 249 " =    1.967
peak=    3.867 closest distance to " CB  TRP A 266 " =    0.923
peak=    3.866 closest distance to " CB  TRP A 179 " =    1.388
peak=    3.855 closest distance to " CB  GLU A 277 " =    3.630
peak=    3.845 closest distance to " CA  ASN A 215 " =    1.217
peak=    3.839 closest distance to " O   MET A 105 " =    1.818
peak=    3.837 closest distance to " O   HOH Z 344 " =    3.135
peak=    3.834 closest distance to " O   HOH Z 158 " =    3.027
peak=    3.833 closest distance to " O   HOH Z 180 " =    2.169
peak=    3.830 closest distance to " O   HOH Z 316 " =    3.119
peak=    3.821 closest distance to " NH1AARG A 145 " =    1.135
peak=    3.816 closest distance to " CB  ARG A 190 " =    1.683
peak=    3.811 closest distance to " CG1 ILE A  33 " =    1.266
peak=    3.808 closest distance to " O   HOH Z  54 " =    1.706
peak=    3.802 closest distance to " O   HOH Z  20 " =    1.788
peak=    3.795 closest distance to " CA  THR A 264 " =    0.882
peak=    3.786 closest distance to " O   HOH Z 193 " =    2.099
peak=    3.776 closest distance to " O   HOH Z  44 " =    1.792
peak=    3.766 closest distance to " O   HOH Z  40 " =    1.724
peak=    3.753 closest distance to " CB  SER A 216 " =    0.826
peak=    3.739 closest distance to " CA  ALA A  51 " =    0.979
peak=    3.729 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.726 closest distance to " CD1 ILE A 106 " =    0.842
peak=    3.724 closest distance to " CD  ARG A 159 " =    0.799
peak=    3.723 closest distance to " ND2 ASN A 110 " =    1.788
peak=    3.722 closest distance to " O   HOH Z 371 " =    3.264
peak=    3.717 closest distance to " O   HOH Z 133 " =    2.375
peak=    3.715 closest distance to " O   HOH Z 147 " =    1.744
peak=    3.709 closest distance to " N   ARG A 156 " =    1.373
peak=    3.705 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.703 closest distance to " O   HOH Z 197 " =    2.789
peak=    3.693 closest distance to " O   TRP A 274 " =    1.834
peak=    3.683 closest distance to " O   HOH Z  49 " =    2.199
peak=    3.680 closest distance to " O   HOH Z 133 " =    1.667
peak=    3.678 closest distance to " CG2 ILE A 120 " =    1.186
peak=    3.667 closest distance to " O   HOH Z  10 " =    1.840
peak=    3.661 closest distance to " O   HOH Z 189 " =    2.383
peak=    3.654 closest distance to " O   HOH Z 280 " =    3.009
peak=    3.653 closest distance to " CB  ALA A 291 " =    1.443
peak=    3.651 closest distance to " O   HOH Z 346 " =    1.663
peak=    3.648 closest distance to " O   HOH Z 272 " =    1.873
peak=    3.646 closest distance to " O   HOH Z 426 " =    1.543
peak=    3.641 closest distance to " CG2 THR A 221 " =    1.021
peak=    3.641 closest distance to " O   HOH Z 203 " =    1.884
peak=    3.640 closest distance to " CA  MET A  40 " =    1.093
peak=    3.638 closest distance to " O   HOH Z 423 " =    1.913
peak=    3.636 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.636 closest distance to " CB  SER A 212 " =    1.137
peak=    3.632 closest distance to " ND1 HIS A  86 " =    1.800
peak=    3.629 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.621 closest distance to " O   HOH Z 411 " =    3.765
peak=    3.619 closest distance to " O   HOH Z 245 " =    1.324
peak=    3.618 closest distance to " O   HOH Z 368 " =    3.654
peak=    3.617 closest distance to " O   HOH Z 193 " =    1.690
peak=    3.607 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.601 closest distance to " ND1 HIS A  81 " =    1.613
peak=    3.597 closest distance to " O   HOH Z 250 " =    1.478
peak=    3.596 closest distance to " O   HOH Z 295 " =    1.465
peak=    3.596 closest distance to " O   HOH Z 214 " =    2.490
peak=    3.593 closest distance to " CB  GLN A  88 " =    1.243
peak=    3.590 closest distance to " CB  LEU A 143 " =    1.099
peak=    3.582 closest distance to " O   HOH Z 172 " =    3.624
peak=    3.581 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.575 closest distance to " O   HOH Z 406 " =    1.627
peak=    3.571 closest distance to " O   HOH Z   1 " =    2.032
peak=    3.568 closest distance to " O   HOH Z 134 " =    1.376
peak=    3.568 closest distance to " CG1BVAL A  72 " =    1.655
peak=    3.567 closest distance to " O   ALA A 165 " =    1.422
peak=    3.564 closest distance to " O   HOH Z  88 " =    3.537
peak=    3.555 closest distance to " CD  ARG A  66 " =    2.427
peak=    3.549 closest distance to " O   HOH Z 374 " =    2.702
peak=    3.544 closest distance to " O   GLY A  57 " =    2.556
peak=    3.543 closest distance to " CA  ASP A 140 " =    1.142
peak=    3.543 closest distance to " O   HOH Z 411 " =    1.842
peak=    3.542 closest distance to " O   HOH Z 305 " =    3.690
peak=    3.541 closest distance to " OG BSER A 164 " =    2.385
peak=    3.539 closest distance to " O   HOH Z  61 " =    1.594
peak=    3.536 closest distance to " O   HOH Z  35 " =    2.639
peak=    3.533 closest distance to " O   SER A  87 " =    2.208
peak=    3.524 closest distance to " O   HOH Z   6 " =    2.215
peak=    3.524 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.501 closest distance to " O   HOH Z  97 " =    1.935
peak=    3.500 closest distance to " CB  MET A  40 " =    0.899
peak=    3.499 closest distance to " CZ  PHE A 192 " =    0.924
peak=    3.497 closest distance to " O   HOH Z 213 " =    1.729
peak=    3.497 closest distance to " NZ  LYS A 166 " =    3.037
peak=    3.493 closest distance to " CB  ARG A 139 " =    0.887
peak=    3.493 closest distance to " CD BLYS A 290 " =    1.071
peak=    3.493 closest distance to " CA  ARG A  36 " =    1.173
peak=    3.492 closest distance to " O   THR A 251 " =    1.210
peak=    3.487 closest distance to " O   HOH Z  68 " =    1.672
peak=    3.485 closest distance to " CD  ARG A 219 " =    1.025
peak=    3.482 closest distance to " O   ALA A   1 " =    1.496
peak=    3.481 closest distance to " CB  ALA A 248 " =    0.953
peak=    3.478 closest distance to " CA  ALA A 291 " =    0.909
peak=    3.470 closest distance to " CB  SER A 141 " =    0.977
peak=    3.468 closest distance to " CG1 ILE A 151 " =    0.986
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.264
peak=    3.463 closest distance to " CB  MET A  47 " =    0.988
peak=    3.456 closest distance to " NZ  LYS A 117 " =    3.336
peak=    3.452 closest distance to " O   HOH Z  68 " =    2.102
peak=    3.451 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.450 closest distance to " O   HOH Z  49 " =    2.501
peak=    3.448 closest distance to " O   HOH Z  59 " =    2.189
peak=    3.442 closest distance to " CA  ASP A 191 " =    0.759
peak=    3.437 closest distance to " O   HOH Z  53 " =    2.547
peak=    3.428 closest distance to " O   HOH Z 227 " =    1.623
peak=    3.421 closest distance to " O   HOH Z 329 " =    3.646
peak=    3.419 closest distance to " N   SER A 135 " =    1.338
peak=    3.414 closest distance to " O   HOH Z 263 " =    1.760
peak=    3.412 closest distance to " CA  ASN A 176 " =    1.233
peak=    3.409 closest distance to " N   ASN A  39 " =    1.335
peak=    3.405 closest distance to " O   HOH Z 425 " =    1.304
peak=    3.404 closest distance to " OD1 ASN A 217 " =    1.699
peak=    3.401 closest distance to " OG  SER A  22 " =    2.760
peak=    3.396 closest distance to " O   HOH Z 273 " =    2.745
peak=    3.394 closest distance to " O   HOH Z  93 " =    2.650
peak=    3.391 closest distance to " CG  MET A 185 " =    1.107
peak=    3.391 closest distance to " O   HOH Z 261 " =    2.102
peak=    3.389 closest distance to " N   ASN A 127 " =    1.244
peak=    3.387 closest distance to " CA  ARG A 195 " =    1.279
peak=    3.384 closest distance to " CA  SER A  87 " =    0.987
peak=    3.380 closest distance to " O   HOH Z  43 " =    1.857
peak=    3.378 closest distance to " CG  LYS A  76 " =    0.956
peak=    3.378 closest distance to " CA  LYS A 117 " =    1.210
peak=    3.376 closest distance to " CB  GLU A  46 " =    1.013
peak=    3.369 closest distance to " O   HOH Z 281 " =    4.516
peak=    3.364 closest distance to " CD2 LEU A 297 " =    0.851
peak=    3.364 closest distance to " OE1 GLU A 277 " =    1.948
peak=    3.364 closest distance to " CB  ILE A 120 " =    1.274
peak=    3.360 closest distance to " CG2BVAL A  41 " =    0.872
peak=    3.360 closest distance to " CA  GLY A 267 " =    1.138
peak=    3.353 closest distance to " CB  ASP A 171 " =    0.759
peak=    3.351 closest distance to " CD2 LEU A 255 " =    1.398
peak=    3.350 closest distance to " O   HOH Z 334 " =    1.524
peak=    3.347 closest distance to " CD  ARG A  66 " =    2.437
peak=    3.344 closest distance to " O   HOH Z 126 " =    2.131
peak=    3.339 closest distance to " CG2 VAL A  78 " =    0.937
peak=    3.336 closest distance to " CB  LEU A 255 " =    0.731
peak=    3.333 closest distance to " O   HOH Z 171 " =    2.187
peak=    3.326 closest distance to " CD  LYS A 119 " =    1.360
peak=    3.326 closest distance to " O   HOH Z 427 " =    3.173
peak=    3.325 closest distance to " O   HOH Z 171 " =    3.922
peak=    3.322 closest distance to " CG  LEU A 167 " =    1.179
peak=    3.321 closest distance to " O   HOH Z 291 " =    1.499
peak=    3.319 closest distance to " O   HOH Z 128 " =    2.203
peak=    3.319 closest distance to " CG  MET A 185 " =    1.158
peak=    3.312 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.306 closest distance to " O   HOH Z 383 " =    1.840
peak=    3.303 closest distance to " CG2 THR A 220 " =    0.894
peak=    3.302 closest distance to " CA  ALA A 154 " =    0.912
peak=    3.299 closest distance to " O   HOH Z 345 " =    3.409
peak=    3.299 closest distance to " O   HOH Z 163 " =    1.528
peak=    3.297 closest distance to " CB  ALA A  71 " =    1.337
peak=    3.295 closest distance to " O   ALA A 158 " =    1.294
peak=    3.295 closest distance to " O   HOH Z 313 " =    1.749
peak=    3.294 closest distance to " CG BARG A 275 " =    1.443
peak=    3.293 closest distance to " O   HOH Z 211 " =    2.665
peak=    3.289 closest distance to " O   HOH Z 271 " =    2.425
peak=    3.289 closest distance to " CA  ALA A 233 " =    1.389
peak=    3.285 closest distance to " O   HOH Z 199 " =    1.563
peak=    3.279 closest distance to " O   HOH Z 391 " =    2.993
peak=    3.273 closest distance to " CB  ALA A  34 " =    1.085
peak=    3.272 closest distance to " CA  ILE A  33 " =    1.603
peak=    3.270 closest distance to " O   HOH Z 183 " =    1.451
peak=    3.269 closest distance to " CB  ALA A 100 " =    1.183
peak=    3.267 closest distance to " O   THR A 220 " =    1.303
peak=    3.264 closest distance to " O   HOH Z 247 " =    1.341
peak=    3.262 closest distance to " O   HOH Z 188 " =    2.179
peak=    3.256 closest distance to " O   HOH Z  54 " =    2.319
peak=    3.249 closest distance to " O   HOH Z 227 " =    2.117
peak=    3.248 closest distance to " CG1 VAL A 202 " =    1.944
peak=    3.240 closest distance to " O   HOH Z 255 " =    1.652
peak=    3.237 closest distance to " CB  TYR A 116 " =    0.926
peak=    3.236 closest distance to " CD1 LEU A  96 " =    0.756
peak=    3.235 closest distance to " O   HOH Z 250 " =    1.526
peak=    3.235 closest distance to " CZ2 TRP A 179 " =    1.687
peak=    3.233 closest distance to " O   HOH Z 163 " =    1.639
peak=    3.231 closest distance to " O   HOH Z 279 " =    2.205
peak=    3.228 closest distance to " CZ  PHE A 208 " =    1.171
peak=    3.225 closest distance to " CD2 HIS A  81 " =    1.211
peak=    3.223 closest distance to " CA  ALA A 248 " =    1.212
peak=    3.223 closest distance to " CB  ASN A 142 " =    1.005
peak=    3.220 closest distance to " O   HOH Z 345 " =    1.754
peak=    3.219 closest distance to " O   HOH Z 108 " =    1.274
peak=    3.215 closest distance to " NH2AARG A 190 " =    1.282
peak=    3.215 closest distance to " CG AARG A 275 " =    1.104
peak=    3.215 closest distance to " O   HOH Z 234 " =    1.760
peak=    3.215 closest distance to " O   HOH Z 281 " =    4.009
peak=    3.211 closest distance to " OG1 THR A 294 " =    1.663
peak=    3.211 closest distance to " N   SER A 134 " =    1.400
peak=    3.210 closest distance to " CD1 ILE A 106 " =    0.892
peak=    3.207 closest distance to " O   HOH Z 388 " =    1.978
peak=    3.206 closest distance to " CG  MET A 113 " =    1.380
peak=    3.204 closest distance to " O   HOH Z 173 " =    1.840
peak=    3.204 closest distance to " O   HOH Z 152 " =    2.075
peak=    3.198 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.187 closest distance to " O   HOH Z 163 " =    1.877
peak=    3.180 closest distance to " CG2 ILE A 106 " =    0.950
peak=    3.176 closest distance to " CA  ASP A 162 " =    1.164
peak=    3.173 closest distance to " O   HOH Z 213 " =    2.247
peak=    3.171 closest distance to " CD2 TRP A 179 " =    1.342
peak=    3.167 closest distance to " CB  PHE A  16 " =    1.042
peak=    3.164 closest distance to " CB  GLU A 152 " =    1.475
peak=    3.162 closest distance to " OG BSER A  99 " =    2.177
peak=    3.160 closest distance to " OD1BASN A 224 " =    2.333
peak=    3.159 closest distance to " O   HOH Z  68 " =    2.616
peak=    3.157 closest distance to " O   HOH Z 116 " =    1.777
peak=    3.153 closest distance to " CB  LYS A 193 " =    0.992
peak=    3.149 closest distance to " O   HOH Z 267 " =    2.108
peak=    3.144 closest distance to " CD1AILE A 234 " =    1.000
peak=    3.144 closest distance to " CA  ASN A  74 " =    1.218
peak=    3.143 closest distance to " CG2 VAL A  67 " =    1.095
peak=    3.141 closest distance to " O   HOH Z 353 " =    2.742
peak=    3.141 closest distance to " CB  ASN A 215 " =    1.160
peak=    3.139 closest distance to " NH1 ARG A 138 " =    1.176
peak=    3.135 closest distance to " CB  SER A  26 " =    1.647
peak=    3.132 closest distance to " O   HOH Z  85 " =    2.168
peak=    3.122 closest distance to " O   HOH Z  63 " =    2.316
peak=    3.121 closest distance to " CG2 VAL A 174 " =    1.367
peak=    3.118 closest distance to " CA  ARG A 195 " =    1.268
peak=    3.116 closest distance to " N   TYR A  15 " =    0.767
peak=    3.109 closest distance to " O   HOH Z 185 " =    1.784
peak=    3.107 closest distance to " NH2AARG A 275 " =    3.710
peak=    3.104 closest distance to " CD  PRO A 243 " =    1.484
peak=    3.095 closest distance to " CG BARG A 102 " =    1.852
peak=    3.089 closest distance to " O   HOH Z 407 " =    2.650
peak=    3.087 closest distance to " CE1 HIS A 115 " =    1.065
peak=    3.085 closest distance to " CB  THR A 157 " =    1.081
peak=    3.084 closest distance to " CA  ALA A 158 " =    1.119
peak=    3.065 closest distance to " NZ  LYS A  76 " =    1.192
peak=    3.055 closest distance to " O   HOH Z 359 " =    1.484
peak=    3.050 closest distance to " O   HOH Z 387 " =    2.973
peak=    3.017 closest distance to " CB  TRP A 179 " =    1.692

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.712 - 5.414
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.712 - 5.414

peak=   -4.868 closest distance to " O   HOH Z 266 " =    4.520
peak=   -4.448 closest distance to " CB  PRO A 243 " =    2.598
peak=   -4.387 closest distance to " CD  ARG A 156 " =    1.989
peak=   -4.270 closest distance to " O   HOH Z 372 " =    2.457
peak=   -4.266 closest distance to " O   HOH Z 198 " =    2.336
peak=   -4.252 closest distance to " O   VAL A  67 " =    2.723
peak=   -4.203 closest distance to " O   ILE A 109 " =    2.677
peak=   -4.188 closest distance to " O   HOH Z 290 " =    1.163
peak=   -4.087 closest distance to " O   HOH Z 126 " =    1.932
peak=   -4.072 closest distance to " O   HOH Z  10 " =    1.528
peak=   -4.039 closest distance to " SG  CYS A 254 " =    3.222
peak=   -4.031 closest distance to " CG  GLN A 223 " =    1.881
peak=   -4.027 closest distance to " N   ALA A  43 " =    2.505
peak=   -4.026 closest distance to " O   HOH Z 353 " =    2.177
peak=   -4.013 closest distance to " O   HOH Z  52 " =    1.388
peak=   -4.004 closest distance to " O   HOH Z 377 " =    2.025
peak=   -3.970 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -3.931 closest distance to " CD1 LEU A 228 " =    2.343
peak=   -3.919 closest distance to " O   HOH Z 231 " =    2.188
peak=   -3.895 closest distance to " O   HOH Z 118 " =    3.028
peak=   -3.894 closest distance to " C   HIS A 108 " =    1.071
peak=   -3.891 closest distance to " CZ3 TRP A 179 " =    1.130
peak=   -3.889 closest distance to " O   HOH Z 407 " =    3.334
peak=   -3.873 closest distance to " OG  SER A  97 " =    2.172
peak=   -3.840 closest distance to " OD1 ASN A 148 " =    1.641
peak=   -3.838 closest distance to " O   PRO A 198 " =    1.306
peak=   -3.834 closest distance to " O   HOH Z 389 " =    1.856
peak=   -3.807 closest distance to " CD1 PHE A  59 " =    1.828
peak=   -3.802 closest distance to " O   HOH Z 185 " =    2.331
peak=   -3.765 closest distance to " CG1 VAL A 250 " =    2.664
peak=   -3.751 closest distance to " O   HOH Z  43 " =    1.550
peak=   -3.750 closest distance to " CD  ARG A 139 " =    1.573
peak=   -3.743 closest distance to " O   HOH Z  38 " =    1.453
peak=   -3.739 closest distance to " NH2AARG A 275 " =    5.414
peak=   -3.738 closest distance to " CG  PHE A 283 " =    2.747
peak=   -3.723 closest distance to " O   PRO A 163 " =    2.085
peak=   -3.722 closest distance to " OG  SER A  62 " =    1.586
peak=   -3.716 closest distance to " CD2 LEU A 300 " =    2.896
peak=   -3.711 closest distance to " CG  ASP A 231 " =    0.834
peak=   -3.693 closest distance to " O   HOH Z 311 " =    3.667
peak=   -3.689 closest distance to " ND2 ASN A  45 " =    1.165
peak=   -3.676 closest distance to " CZ  TYR A 169 " =    1.753
peak=   -3.675 closest distance to " C   ALA A 158 " =    1.273
peak=   -3.673 closest distance to " OG BSER A 134 " =    1.770
peak=   -3.668 closest distance to " CB  ASN A  39 " =    2.217
peak=   -3.630 closest distance to " CA  GLY A 203 " =    2.273
peak=   -3.622 closest distance to " CB  ILE A 239 " =    1.999
peak=   -3.611 closest distance to " NE2 GLN A  88 " =    1.904
peak=   -3.611 closest distance to " CG1 VAL A 112 " =    2.795
peak=   -3.588 closest distance to " OG BSER A 134 " =    1.206
peak=   -3.584 closest distance to " N   THR A 157 " =    1.627
peak=   -3.580 closest distance to " N   SER A 212 " =    2.025
peak=   -3.576 closest distance to " NH1 ARG A 195 " =    2.570
peak=   -3.574 closest distance to " CG  ARG A 269 " =    2.428
peak=   -3.574 closest distance to " CD2 TYR A 293 " =    2.033
peak=   -3.573 closest distance to " C   ASN A 285 " =    2.476
peak=   -3.570 closest distance to " O   HOH Z  73 " =    2.286
peak=   -3.570 closest distance to " CD1 LEU A 101 " =    2.458
peak=   -3.565 closest distance to " O   GLY A 211 " =    1.509
peak=   -3.564 closest distance to " O   HOH Z 292 " =    4.593
peak=   -3.563 closest distance to " CZ  PHE A  59 " =    1.647
peak=   -3.557 closest distance to " O   HOH Z 435 " =    2.756
peak=   -3.551 closest distance to " CD  ARG A 195 " =    5.168
peak=   -3.550 closest distance to " SG ACYS A 201 " =    1.983
peak=   -3.545 closest distance to " O   HOH Z 351 " =    1.420
peak=   -3.538 closest distance to " O   HOH Z  11 " =    1.788
peak=   -3.537 closest distance to " O   HOH Z  98 " =    2.145
peak=   -3.534 closest distance to " OXT GLY A 302 " =    2.849
peak=   -3.504 closest distance to " CD  GLN A  58 " =    1.125
peak=   -3.489 closest distance to " CG1 VAL A 112 " =    2.580
peak=   -3.488 closest distance to " CG1 VAL A 112 " =    2.906
peak=   -3.486 closest distance to " O   HOH Z  93 " =    1.791
peak=   -3.466 closest distance to " O   HOH Z  76 " =    1.861
peak=   -3.460 closest distance to " O   HOH Z 211 " =    1.688
peak=   -3.449 closest distance to " O   HOH Z 417 " =    2.569
peak=   -3.449 closest distance to " CE  MET A  93 " =    1.249
peak=   -3.446 closest distance to " O   VAL A 153 " =    2.291
peak=   -3.443 closest distance to " CB  ALA A 291 " =    2.340
peak=   -3.442 closest distance to " CD1 LEU A 297 " =    2.416
peak=   -3.441 closest distance to " CG1 VAL A 197 " =    2.283
peak=   -3.440 closest distance to " O   HOH Z 275 " =    1.553
peak=   -3.438 closest distance to " CG  ARG A  66 " =    2.287
peak=   -3.436 closest distance to " O   GLY A 196 " =    1.131
peak=   -3.435 closest distance to " CA  GLY A 241 " =    3.049
peak=   -3.434 closest distance to " O   HOH Z  19 " =    2.467
peak=   -3.428 closest distance to " CG2 VAL A 189 " =    2.082
peak=   -3.424 closest distance to " O   HOH Z 198 " =    1.382
peak=   -3.422 closest distance to " CB  PRO A 163 " =    2.624
peak=   -3.419 closest distance to " N   ALA A 226 " =    2.119
peak=   -3.418 closest distance to " ND2 ASN A 249 " =    2.150
peak=   -3.416 closest distance to " O   HOH Z  13 " =    1.481
peak=   -3.416 closest distance to " OD2 ASP A 171 " =    1.830
peak=   -3.412 closest distance to " NH2 ARG A  79 " =    1.892
peak=   -3.410 closest distance to " CB  ASP A 132 " =    2.274
peak=   -3.400 closest distance to " C   LEU A 143 " =    1.168
peak=   -3.398 closest distance to " CB  PHE A 192 " =    2.084
peak=   -3.394 closest distance to " OE1 GLN A  88 " =    1.209
peak=   -3.393 closest distance to " OD1 ASP A 191 " =    1.686
peak=   -3.392 closest distance to " CG  GLU A  53 " =    1.376
peak=   -3.384 closest distance to " O   HOH Z 388 " =    2.000
peak=   -3.381 closest distance to " CE  MET A 105 " =    2.147
peak=   -3.380 closest distance to " CB  ALA A 291 " =    2.244
peak=   -3.377 closest distance to " CG2 ILE A 263 " =    2.335
peak=   -3.368 closest distance to " O   HOH Z 252 " =    4.236
peak=   -3.368 closest distance to " O   HOH Z 393 " =    1.451
peak=   -3.365 closest distance to " O   VAL A  67 " =    2.619
peak=   -3.358 closest distance to " O   VAL A 125 " =    2.294
peak=   -3.358 closest distance to " O   HOH Z  88 " =    2.221
peak=   -3.355 closest distance to " NH2 ARG A 159 " =    2.406
peak=   -3.354 closest distance to " NH2 ARG A  66 " =    2.019
peak=   -3.347 closest distance to " O   HOH Z 313 " =    2.039
peak=   -3.347 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.336 closest distance to " CB  TYR A  15 " =    2.228
peak=   -3.327 closest distance to " O   HOH Z 166 " =    1.542
peak=   -3.321 closest distance to " CG  TRP A 266 " =    1.786
peak=   -3.317 closest distance to " OE2 GLU A   2 " =    1.731
peak=   -3.314 closest distance to " CB  ASP A 286 " =    2.147
peak=   -3.314 closest distance to " CA  ASP A 298 " =    1.062
peak=   -3.309 closest distance to " CB  ALA A  43 " =    2.488
peak=   -3.304 closest distance to " O   HOH Z 436 " =    1.449
peak=   -3.303 closest distance to " N   GLN A  58 " =    1.704
peak=   -3.302 closest distance to " O   HOH Z 298 " =    2.687
peak=   -3.302 closest distance to " O   HOH Z 166 " =    1.803
peak=   -3.300 closest distance to " O   HOH Z 111 " =    2.101
peak=   -3.300 closest distance to " CD  LYS A 289 " =    2.558
peak=   -3.297 closest distance to " CB  TRP A  85 " =    2.458
peak=   -3.294 closest distance to " ND2 ASN A  60 " =    1.483
peak=   -3.294 closest distance to " O   HOH Z  97 " =    1.838
peak=   -3.291 closest distance to " O   HOH Z 243 " =    2.106
peak=   -3.284 closest distance to " O   HOH Z 394 " =    1.481
peak=   -3.283 closest distance to " O   HOH Z  60 " =    2.563
peak=   -3.282 closest distance to " O   HOH Z 196 " =    2.076
peak=   -3.274 closest distance to " CB  ALA A 248 " =    2.031
peak=   -3.273 closest distance to " O   HOH Z 266 " =    4.905
peak=   -3.267 closest distance to " CB  PHE A 208 " =    2.243
peak=   -3.265 closest distance to " OG1 THR A 178 " =    1.286
peak=   -3.262 closest distance to " O   HOH Z 222 " =    1.236
peak=   -3.259 closest distance to " O   HOH Z 241 " =    1.259
peak=   -3.254 closest distance to " O   VAL A 189 " =    2.554
peak=   -3.253 closest distance to " CD1 ILE A 239 " =    2.330
peak=   -3.253 closest distance to " CD2 PHE A  61 " =    2.417
peak=   -3.245 closest distance to " O   ASP A 231 " =    2.664
peak=   -3.241 closest distance to " CB  CYS A 254 " =    2.311
peak=   -3.240 closest distance to " CG  LEU A  83 " =    1.888
peak=   -3.239 closest distance to " O   HOH Z  37 " =    1.908
peak=   -3.238 closest distance to " OD1 ASP A 191 " =    1.550
peak=   -3.228 closest distance to " CB  ASP A 132 " =    2.292
peak=   -3.224 closest distance to " NE2 GLN A  58 " =    1.147
peak=   -3.223 closest distance to " O   HOH Z 385 " =    1.970
peak=   -3.222 closest distance to " N   SER A 276 " =    1.309
peak=   -3.221 closest distance to " CE2 PHE A 218 " =    2.443
peak=   -3.216 closest distance to " O   HOH Z 278 " =    1.774
peak=   -3.215 closest distance to " O   SER A 135 " =    1.529
peak=   -3.214 closest distance to " N   THR A 235 " =    1.341
peak=   -3.207 closest distance to " O   HOH Z   6 " =    2.071
peak=   -3.207 closest distance to " O   HOH Z 207 " =    2.167
peak=   -3.206 closest distance to " CH2 TRP A 177 " =    2.116
peak=   -3.204 closest distance to " O   HOH Z 168 " =    1.830
peak=   -3.201 closest distance to " O   HOH Z 317 " =    2.450
peak=   -3.195 closest distance to " O   HOH Z 298 " =    1.191
peak=   -3.194 closest distance to " CG  GLU A 277 " =    1.166
peak=   -3.193 closest distance to " O   MET A  40 " =    2.817
peak=   -3.190 closest distance to " N   GLN A 122 " =    1.510
peak=   -3.188 closest distance to " C   SER A 206 " =    1.565
peak=   -3.187 closest distance to " NE1 TRP A 266 " =    2.279
peak=   -3.186 closest distance to " C   MET A 188 " =    1.452
peak=   -3.183 closest distance to " CG  PRO A 163 " =    2.545
peak=   -3.182 closest distance to " CE  LYS A  76 " =    2.757
peak=   -3.181 closest distance to " O   HOH Z 426 " =    1.601
peak=   -3.180 closest distance to " CG2 ILE A  20 " =    2.867
peak=   -3.180 closest distance to " CG  ASP A  50 " =    2.468
peak=   -3.168 closest distance to " O   HOH Z   6 " =    1.599
peak=   -3.164 closest distance to " CA  SER A 135 " =    1.327
peak=   -3.159 closest distance to " NH2 ARG A  79 " =    1.596
peak=   -3.153 closest distance to " O   HOH Z 234 " =    4.266
peak=   -3.152 closest distance to " O   HOH Z 396 " =    1.770
peak=   -3.151 closest distance to " CE3 TRP A 274 " =    2.517
peak=   -3.147 closest distance to " O   PHE A 218 " =    1.594
peak=   -3.146 closest distance to " O   HOH Z 281 " =    2.639
peak=   -3.144 closest distance to " CA  GLY A 241 " =    2.251
peak=   -3.143 closest distance to " O   VAL A 174 " =    2.079
peak=   -3.140 closest distance to " O   ALA A 161 " =    1.619
peak=   -3.139 closest distance to " O   HOH Z 262 " =    2.778
peak=   -3.134 closest distance to " CD  GLN A  88 " =    0.831
peak=   -3.133 closest distance to " N   ALA A 248 " =    1.603
peak=   -3.125 closest distance to " CE3 TRP A 150 " =    2.051
peak=   -3.114 closest distance to " O   PRO A 198 " =    2.089
peak=   -3.110 closest distance to " CE1 TYR A 169 " =    2.442
peak=   -3.106 closest distance to " C   LEU A 222 " =    0.712
peak=   -3.097 closest distance to " N   ALA A   9 " =    1.546
peak=   -3.092 closest distance to " CG  ASN A 301 " =    1.949
peak=   -3.091 closest distance to " O   ASN A 301 " =    1.493
peak=   -3.082 closest distance to " CD2 LEU A 237 " =    2.669
peak=   -3.081 closest distance to " CB  ALA A   9 " =    2.569
peak=   -3.073 closest distance to " O   HOH Z 174 " =    3.074
peak=   -3.067 closest distance to " O   HOH Z 323 " =    1.345
peak=   -3.064 closest distance to " O   GLY A  80 " =    2.446
peak=   -3.059 closest distance to " OD1 ASP A 200 " =    1.431
peak=   -3.054 closest distance to " O   HOH Z 371 " =    1.958
peak=   -3.038 closest distance to " OXT GLY A 302 " =    3.209
peak=   -3.038 closest distance to " CA  GLY A 241 " =    2.775
peak=   -3.036 closest distance to " O   HOH Z 350 " =    1.802

================= 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    :  0.3534 0.3591   6.101418e+00   6.110787e+00
   1_bss:  0.3423 0.3482   6.087282e+00   6.087227e+00
   1_xyz:  0.1947 0.2197   5.587140e+00   5.699287e+00
   1_adp:  0.1777 0.2239   5.532354e+00   5.719240e+00
   1_occ:  0.1773 0.2244   5.531165e+00   5.718326e+00
   2_bss:  0.1753 0.2218   5.527128e+00   5.711621e+00
   2_xyz:  0.1307 0.1730   5.271129e+00   5.488402e+00
   2_adp:  0.1245 0.1650   5.224921e+00   5.441446e+00
   2_occ:  0.1243 0.1647   5.224037e+00   5.440583e+00
   3_bss:  0.1247 0.1650   5.225649e+00   5.441031e+00
   3_xyz:  0.1127 0.1561   5.148032e+00   5.382451e+00
   3_adp:  0.1105 0.1556   5.137670e+00   5.378098e+00
   3_occ:  0.1104 0.1555   5.137615e+00   5.378323e+00
   4_bss:  0.1104 0.1555   5.137500e+00   5.378216e+00
   4_xyz:  0.1077 0.1560   5.128007e+00   5.377720e+00
   4_adp:  0.1073 0.1565   5.128014e+00   5.380443e+00
   4_occ:  0.1072 0.1565   5.128066e+00   5.380742e+00
   5_bss:  0.1072 0.1565   5.128130e+00   5.380784e+00
   5_xyz:  0.1084 0.1572   5.136333e+00   5.387132e+00
   5_adp:  0.1084 0.1574   5.136850e+00   5.388686e+00
   5_occ:  0.1083 0.1574   5.136919e+00   5.388950e+00
   5_bss:  0.1083 0.1574   5.136978e+00   5.388984e+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:  0.318  41.555  -0.133  -1.902   0.857  -0.000   0.000   0.000
   1_xyz:  0.318  41.555  -0.133  -1.902   0.857  -0.000   0.000   0.000
   1_adp:  0.318  41.555  -0.133  -1.902   0.857  -0.000   0.000   0.000
   1_occ:  0.318  41.555  -0.133  -1.902   0.857  -0.000   0.000   0.000
   2_bss:  0.330  54.716  -1.906  -2.553  -1.365  -0.000  -0.000  -0.000
   2_xyz:  0.330  54.716  -1.906  -2.553  -1.365  -0.000  -0.000  -0.000
   2_adp:  0.330  54.716  -1.906  -2.553  -1.365  -0.000  -0.000  -0.000
   2_occ:  0.330  54.716  -1.906  -2.553  -1.365  -0.000  -0.000  -0.000
   3_bss:  0.330  54.716  -2.304  -2.535  -1.794  -0.000  -0.000  -0.000
   3_xyz:  0.330  54.716  -2.304  -2.535  -1.794  -0.000  -0.000  -0.000
   3_adp:  0.330  54.716  -2.304  -2.535  -1.794  -0.000  -0.000  -0.000
   3_occ:  0.330  54.716  -2.304  -2.535  -1.794  -0.000  -0.000  -0.000
   4_bss:  0.330  54.716  -2.313  -2.403  -1.855  -0.000  -0.000  -0.000
   4_xyz:  0.330  54.716  -2.313  -2.403  -1.855  -0.000  -0.000  -0.000
   4_adp:  0.330  54.716  -2.313  -2.403  -1.855  -0.000  -0.000  -0.000
   4_occ:  0.330  54.716  -2.313  -2.403  -1.855  -0.000  -0.000  -0.000
   5_bss:  0.330  54.716  -2.191  -2.248  -1.731  -0.000  -0.000  -0.000
   5_xyz:  0.330  54.716  -2.191  -2.248  -1.731  -0.000  -0.000  -0.000
   5_adp:  0.330  54.716  -2.191  -2.248  -1.731  -0.000  -0.000  -0.000
   5_occ:  0.330  54.716  -2.191  -2.248  -1.731  -0.000  -0.000  -0.000
   5_bss:  0.330  54.668  -2.053  -2.075  -1.573  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.788 0.6588  0.8405    37052.140
   1_bss:  37.539 0.6711  0.8492    33870.022
   1_xyz:  21.142 0.8521  1.0083    12565.378
   1_adp:  21.829 0.8444  1.0046    13029.850
   1_occ:  21.830 0.8443  1.0044    13002.767
   2_bss:  21.593 0.8465  0.9523    12769.495
   2_xyz:  16.349 0.8948  0.9805     7870.440
   2_adp:  15.171 0.9054  0.9835     7171.912
   2_occ:  15.150 0.9056  0.9834     7155.047
   3_bss:  15.166 0.9055  0.9732     7181.881
   3_xyz:  13.987 0.9150  0.9775     6324.276
   3_adp:  13.864 0.9162  0.9744     6263.291
   3_occ:  13.865 0.9162  0.9743     6265.807
   4_bss:  13.863 0.9162  0.9749     6264.512
   4_xyz:  13.835 0.9164  0.9741     6254.001
   4_adp:  13.864 0.9163  0.9700     6283.077
   4_occ:  13.869 0.9162  0.9699     6285.797
   5_bss:  13.871 0.9162  0.9745     6286.319
   5_xyz:  13.975 0.9154  0.9737     6360.817
   5_adp:  14.010 0.9151  0.9692     6381.826
   5_occ:  14.013 0.9151  0.9691     6384.067
   5_bss:  14.015 0.9151  0.9728     6384.359
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6493e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6493e-01
   1_xyz:   1.154  0.009  0.073 15.128  0.005  4.116   7.8640e-02
   1_adp:   1.154  0.009  0.073 15.128  0.005  4.116   7.8640e-02
   1_occ:   1.154  0.009  0.073 15.128  0.005  4.116   7.8640e-02
   2_bss:   1.154  0.009  0.073 15.128  0.005  4.116   7.8640e-02
   2_xyz:   1.032  0.007  0.074 14.804  0.004  4.125   6.1680e-02
   2_adp:   1.032  0.007  0.074 14.804  0.004  4.125   6.1680e-02
   2_occ:   1.032  0.007  0.074 14.804  0.004  4.125   6.1680e-02
   3_bss:   1.032  0.007  0.074 14.804  0.004  4.125   6.1680e-02
   3_xyz:   1.084  0.009  0.080 15.145  0.004  4.130   7.0320e-02
   3_adp:   1.084  0.009  0.080 15.145  0.004  4.130   7.0320e-02
   3_occ:   1.084  0.009  0.080 15.145  0.004  4.130   7.0320e-02
   4_bss:   1.084  0.009  0.080 15.145  0.004  4.130   7.0320e-02
   4_xyz:   1.102  0.009  0.081 15.172  0.005  4.131   7.2239e-02
   4_adp:   1.102  0.009  0.081 15.172  0.005  4.131   7.2239e-02
   4_occ:   1.102  0.009  0.081 15.172  0.005  4.131   7.2239e-02
   5_bss:   1.102  0.009  0.081 15.172  0.005  4.131   7.2239e-02
   5_xyz:   1.036  0.008  0.077 14.999  0.004  4.112   6.4817e-02
   5_adp:   1.036  0.008  0.077 14.999  0.004  4.112   6.4817e-02
   5_occ:   1.036  0.008  0.077 14.999  0.004  4.112   6.4817e-02
   5_bss:   1.036  0.008  0.077 14.999  0.004  4.112   6.4817e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4133e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4133e-01
   1_xyz:   9.073  0.054  0.300 89.970  0.034  2.265   1.5732e-01
   1_adp:   9.073  0.054  0.300 89.970  0.034  2.265   1.5732e-01
   1_occ:   9.073  0.054  0.300 89.970  0.034  2.265   1.5732e-01
   2_bss:   9.073  0.054  0.300 89.970  0.034  2.265   1.5732e-01
   2_xyz:   6.939  0.043  0.237 83.623  0.043  2.354   5.3250e-02
   2_adp:   6.939  0.043  0.237 83.623  0.043  2.354   5.3250e-02
   2_occ:   6.939  0.043  0.237 83.623  0.043  2.354   5.3250e-02
   3_bss:   6.939  0.043  0.237 83.623  0.043  2.354   5.3250e-02
   3_xyz:   7.183  0.042  0.242 83.803  0.040  2.274   5.8855e-02
   3_adp:   7.183  0.042  0.242 83.803  0.040  2.274   5.8855e-02
   3_occ:   7.183  0.042  0.242 83.803  0.040  2.274   5.8855e-02
   4_bss:   7.183  0.042  0.242 83.803  0.040  2.274   5.8855e-02
   4_xyz:   7.257  0.042  0.257 82.963  0.040  2.304   5.5441e-02
   4_adp:   7.257  0.042  0.257 82.963  0.040  2.304   5.5441e-02
   4_occ:   7.257  0.042  0.257 82.963  0.040  2.304   5.5441e-02
   5_bss:   7.257  0.042  0.257 82.963  0.040  2.304   5.5441e-02
   5_xyz:   7.095  0.042  0.241 83.678  0.039  2.329   4.5185e-02
   5_adp:   7.095  0.042  0.241 83.678  0.039  2.329   4.5185e-02
   5_occ:   7.095  0.042  0.241 83.678  0.039  2.329   4.5185e-02
   5_bss:   7.095  0.042  0.241 83.678  0.039  2.329   4.5185e-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:  76.90   0.00  17.34  74.59   0.00  13.19  76.90   6.64  39.98
   1_occ:  76.90   0.00  17.34  74.59   0.00  13.19  76.90   6.64  39.98
   2_bss:  76.90   0.00  17.34  74.59   0.00  13.19  76.90   6.64  39.98
   2_xyz:  76.90   0.00  17.34  74.59   0.00  13.19  76.90   6.64  39.98
   2_adp:  76.97   2.44  17.10  76.97   2.44  13.06  76.55   5.56  39.11
   2_occ:  76.97   2.44  17.10  76.97   2.44  13.06  76.55   5.56  39.11
   3_bss:  76.97   2.44  17.10  76.97   2.44  13.06  76.55   5.56  39.11
   3_xyz:  76.97   2.44  17.10  76.97   2.44  13.06  76.55   5.56  39.11
   3_adp:  80.64   1.73  17.06  80.64   1.73  13.01  76.23   5.97  39.10
   3_occ:  80.64   1.73  17.06  80.64   1.73  13.01  76.23   5.97  39.10
   4_bss:  80.64   1.73  17.06  80.64   1.73  13.01  76.23   5.97  39.10
   4_xyz:  80.64   1.73  17.06  80.64   1.73  13.01  76.23   5.97  39.10
   4_adp:  81.38   1.69  16.91  81.38   1.69  12.89  76.07   6.48  38.84
   4_occ:  81.38   1.69  16.91  81.38   1.69  12.89  76.07   6.48  38.84
   5_bss:  81.38   1.69  16.91  81.38   1.69  12.89  76.07   6.48  38.84
   5_xyz:  81.38   1.69  16.91  81.38   1.69  12.89  76.07   6.48  38.84
   5_adp:  83.58   1.35  16.75  83.58   1.35  12.77  75.70   6.35  38.41
   5_occ:  83.58   1.35  16.75  83.58   1.35  12.77  75.70   6.35  38.41
   5_bss:  83.54   1.30  16.70  83.54   1.30  12.72  75.65   6.30  38.37
------------------------------------------------------------------------
 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:    1.482    0.020    0.339
   1_adp:    1.482    0.020    0.339
   1_occ:    1.482    0.020    0.339
   2_bss:    1.482    0.020    0.339
   2_xyz:    0.891    0.034    0.398
   2_adp:    0.891    0.034    0.398
   2_occ:    0.891    0.034    0.398
   3_bss:    0.891    0.034    0.398
   3_xyz:    0.869    0.051    0.438
   3_adp:    0.869    0.051    0.438
   3_occ:    0.869    0.051    0.438
   4_bss:    0.869    0.051    0.438
   4_xyz:    0.977    0.078    0.451
   4_adp:    0.977    0.078    0.451
   4_occ:    0.977    0.078    0.451
   5_bss:    0.977    0.078    0.451
   5_xyz:    1.074    0.081    0.455
   5_adp:    1.074    0.081    0.455
   5_occ:    1.074    0.081    0.455
   5_bss:    1.074    0.081    0.455
------------------------------------------------------------------------

CPU time actual refinement: 355.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/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_1036/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1036/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 355.12 
  Macro-tasks:
    bulk solvent and scale       = 38.75  
    individual site refinement   = 156.12 
    weights calculation          = 29.95  
    collect and process          = 6.70   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 231.65 
  Micro-tasks:
    mask                            = 1.23   
    f_calc                          = 115.78 
    alpha_beta                      = 8.05   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 126.91 
    fmodel                         = 6.86   
    r_factors                      = 0.19   
    phase_errors                   = 11.06  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 271.48 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.876 micro seconds
Total CPU time: 6.15 minutes
from_scatterers_fft:    682 calls, 115.43 s
gradients_fft:          627 calls, 112.00 s

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

# Date 2008-01-16 Time 06:17:05 PST -0800 (1200493025.19 s)
Start R-work = 0.3534, R-free = 0.3591 (no bulk solvent and anisotropic scale)
Final R-work = 0.1323, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.3423, R-free = 0.3482
Final R-work = 0.1083, R-free = 0.1574