# Date 2008-01-16 Time 05:59:30 PST -0800 (1200491970.19 s)
#phil __OFF__

Command line arguments: "../963.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6727
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 963

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 48.1033, 86.822, 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: 3.26, 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: (70.9525, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01123
Completeness in resolution range: 0.963931
Completeness with d_max=infinity: 0.960905

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   2.0112

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01123
Completeness in resolution range: 0.963931
Completeness with d_max=infinity: 0.960905

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.3029 [2132/2160]  1920   212   9.9%
  bin  2:  4.3029 -  3.4284 [2041/2060]  1836   205  10.0%
  bin  3:  3.4284 -  2.9989 [2029/2049]  1827   202  10.0%
  bin  4:  2.9989 -  2.7265 [2000/2025]  1802   198   9.9%
  bin  5:  2.7265 -  2.5320 [1991/2010]  1789   202  10.1%
  bin  6:  2.5320 -  2.3833 [1981/2026]  1787   194   9.8%
  bin  7:  2.3833 -  2.2644 [1975/2009]  1773   202  10.2%
  bin  8:  2.2644 -  2.1661 [1956/1991]  1757   199  10.2%
  bin  9:  2.1661 -  2.0829 [1955/1983]  1763   192   9.8%
  bin 10:  2.0829 -  2.0112 [1529/2009]  1376   153  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 5
        2.22 -     2.89: 1275
        2.89 -     3.56: 4367
        3.56 -     4.23: 9016
        4.23 -     4.90: 13108
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.545 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.734 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.957 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27766 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_963/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 48.10325 86.82195 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: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4281   r_free= 0.4085   ksol= 0.00   Bsol= 0.00   scale= 0.896    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.246127                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7989 0.99   1382  155 0.3499 0.3680      6.5147      6.5067|
|  2:  4.7989 -  3.8294 0.99   1338  145 0.3763 0.3866      6.8081      6.7946|
|  3:  3.8294 -  3.3514 0.99   1307  150 0.4016 0.3500      6.6561      6.5462|
|  4:  3.3514 -  3.0477 0.99   1302  141 0.4203 0.3889      6.4965      6.4128|
|  5:  3.0477 -  2.8308 0.99   1284  142 0.4518 0.4233      6.3544      6.3609|
|  6:  2.8308 -  2.6648 0.98   1290  143 0.4558 0.4270      6.2459      6.1287|
|  7:  2.6648 -  2.5320 0.99   1271  143 0.4566 0.3866       6.217      6.0784|
|  8:  2.5320 -  2.4222 0.98   1276  138 0.4653 0.4302      6.1426        6.15|
|  9:  2.4222 -  2.3293 0.98   1282  145 0.4610 0.4722      6.0773      6.1321|
| 10:  2.3293 -  2.2492 0.98   1237  138 0.4643 0.4140      6.0833      5.9849|
| 11:  2.2492 -  2.1791 0.99   1271  145 0.4696 0.4233      6.0224      5.9973|
| 12:  2.1791 -  2.1170 0.98   1276  133 0.4727 0.5010       5.957      6.0263|
| 13:  2.1170 -  2.0614 0.97   1237  143 0.4640 0.4404      5.8477      5.8206|
| 14:  2.0614 -  2.0112 0.68    877   98 0.4493 0.4748       5.801      5.7551|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7989  1382   155  0.71  33.42   0.83     0.75      68568.85|
|  2:  4.7989 -  3.8294  1338   145  0.75  30.91   0.90     0.82      84506.50|
|  3:  3.8294 -  3.3514  1307   150  0.68  36.91   0.90     0.83      87164.23|
|  4:  3.3514 -  3.0477  1302   141  0.63  41.76   0.90     0.78      75561.41|
|  5:  3.0477 -  2.8308  1284   142  0.56  47.29   0.90     0.73      61403.09|
|  6:  2.8308 -  2.6648  1290   143  0.55  47.73   0.89     0.71      49378.93|
|  7:  2.6648 -  2.5320  1271   143  0.55  47.89   0.93     0.71      44596.75|
|  8:  2.5320 -  2.4222  1276   138  0.54  48.95   0.93     0.71      41876.44|
|  9:  2.4222 -  2.3293  1282   145  0.53  49.88   0.91     0.72      40002.66|
| 10:  2.3293 -  2.2492  1237   138  0.53  49.59   0.95     0.72      36550.27|
| 11:  2.2492 -  2.1791  1271   145  0.52  51.06   0.94     0.72      35099.90|
| 12:  2.1791 -  2.1170  1276   133  0.48  53.75   0.96     0.69      34374.89|
| 13:  2.1170 -  2.0614  1237   143  0.45  56.46   0.92     0.64      31140.56|
| 14:  2.0614 -  2.0112   877    98  0.45  56.01   0.96     0.59      24801.46|
|alpha:            min =        0.59 max =            0.83 mean =         0.73|
|beta:             min =    24801.46 max =        87164.23 mean =     52072.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.14|
|phase err.(test): min =        0.00 max =           89.88 mean =        46.19|
|-----------------------------------------------------------------------------|

============================== 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 = 6.022621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.811   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.495063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.022   (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 |  1.545 -  1.881:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.881 -  2.216:        1 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.216 -  2.552:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.552 -  2.887:     1252 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.887 -  3.223:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.223 -  3.558:     2504 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.558 -  3.894:     4579 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.894 -  4.229:     4437 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.229 -  4.564:     5949 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7159 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.545 |       0.215 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    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: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4281   r_free= 0.4085   ksol= 0.00   Bsol= 0.00   scale= 0.896    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.246127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4172   r_free= 0.3977   ksol= 0.30   Bsol= 50.00   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,5.56,-1.50,0.00,-0.00,-0.00); trace/3= 0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.235094                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.465429              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.738032              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.915   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4172      final r-factor (work) = 0.3485          |
| start r-factor (free) = 0.3977      final r-factor (free) = 0.3701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2001 = 5.47 * 0.50 * 6.2329 + 1.00 * 0.1674                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8171 = 5.47 * 0.50 * 6.1185 + 1.00 * 0.0969                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3485      final r-factor (work) = 0.3235          |
| start r-factor (free) = 0.3701      final r-factor (free) = 0.3775          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5218 = 0.74 * 1.00 * 6.1185 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5001 = 0.74 * 1.00 * 6.0595 + 1.00 * 0.0280                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.02   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    76.02   17.22    None  None   None       |
|    Sol.    : 438    0      0.00    71.90   35.33    None  None   None       |
|    Mac.    : 2385   0      0.00    76.02   13.89    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:     0.000 -   7.602:  675   |   5:    38.008 -  45.610:  110        |
|      1:     7.602 -  15.203:  861   |   6:    45.610 -  53.211:   71        |
|      2:    15.203 -  22.805:  585   |   7:    53.211 -  60.813:   47        |
|      3:    22.805 -  30.407:  295   |   8:    60.813 -  68.415:    8        |
|      4:    30.407 -  38.008:  169   |   9:    68.415 -  76.016:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3235 r_free = 0.3775             target_work(ml) = 6.063         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3230 r_free = 0.3768             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3230   r_free= 0.3768   ksol= 0.30   Bsol= 50.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,5.56,-1.50,0.00,-0.00,-0.00); trace/3= 0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.061802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3226   r_free= 0.3763   ksol= 0.30   Bsol= 50.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.41,-0.58,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.063824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.437269              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.490   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.926443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.851   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3226      final r-factor (work) = 0.2713          |
| start r-factor (free) = 0.3763      final r-factor (free) = 0.3174          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5752 = 5.44 * 0.50 * 6.0612 + 1.00 * 0.0969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3480 = 5.44 * 0.50 * 5.9825 + 1.00 * 0.0839                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2713      final r-factor (work) = 0.2573          |
| start r-factor (free) = 0.3174      final r-factor (free) = 0.3177          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5800 = 0.93 * 1.00 * 5.9825 + 1.00 * 0.0375                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4713 = 0.93 * 1.00 * 5.8870 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.60   18.12    None  None   None       |
|    all(noH): 2823   0      0.00    94.60   18.12    None  None   None       |
|    Sol.    : 438    0      0.18    87.28   38.03    None  None   None       |
|    Mac.    : 2385   0      0.00    94.60   14.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.460:  963   |   5:    47.299 -  56.759:   74        |
|      1:     9.460 -  18.920:  891   |   6:    56.759 -  66.219:   56        |
|      2:    18.920 -  28.380:  416   |   7:    66.219 -  75.679:   33        |
|      3:    28.380 -  37.840:  234   |   8:    75.679 -  85.139:   15        |
|      4:    37.840 -  47.299:  138   |   9:    85.139 -  94.599:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2573 r_free = 0.3177             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2571 r_free = 0.3177             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2571   r_free= 0.3177   ksol= 0.30   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,3.41,-0.58,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.890396                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2570   r_free= 0.3169   ksol= 0.31   Bsol= 65.41   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,2.56,0.23,0.00,0.00,0.00); trace/3= 0.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.892484                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.009481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.911   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.331093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.994  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2570      final r-factor (work) = 0.2196          |
| start r-factor (free) = 0.3169      final r-factor (free) = 0.2774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8901 = 4.01 * 0.50 * 5.8891 + 1.00 * 0.0839                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7286 = 4.01 * 0.50 * 5.8181 + 1.00 * 0.0649                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2196      final r-factor (work) = 0.2097          |
| start r-factor (free) = 0.2774      final r-factor (free) = 0.2607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9438 = 0.33 * 1.00 * 5.8181 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9044 = 0.33 * 1.00 * 5.7196 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.47   16.88    None  None   None       |
|    all(noH): 2823   0      0.00    91.47   16.88    None  None   None       |
|    Sol.    : 438    0      1.57    86.84   38.05    None  None   None       |
|    Mac.    : 2385   0      0.00    91.47   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.147: 1069   |   5:    45.736 -  54.883:   86        |
|      1:     9.147 -  18.294:  938   |   6:    54.883 -  64.031:   54        |
|      2:    18.294 -  27.442:  325   |   7:    64.031 -  73.178:   23        |
|      3:    27.442 -  36.589:  174   |   8:    73.178 -  82.325:   18        |
|      4:    36.589 -  45.736:  132   |   9:    82.325 -  91.472:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2097 r_free = 0.2607             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2095 r_free = 0.2605             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2095   r_free= 0.2605   ksol= 0.31   Bsol= 65.41   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,2.56,0.23,0.00,0.00,0.00); trace/3= 0.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.695158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2094   r_free= 0.2600   ksol= 0.33   Bsol= 74.79   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,1.20,0.03,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.695096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.999276              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.620  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.474599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.284  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2094      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.1988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3634 = 5.00 * 0.50 * 5.7202 + 1.00 * 0.0649                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0187 = 5.00 * 0.50 * 5.5754 + 1.00 * 0.0822                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1592      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6567 = 0.47 * 1.00 * 5.5754 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5673 = 0.47 * 1.00 * 5.3849 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.63   16.71    None  None   None       |
|    all(noH): 2823   0      0.00    97.63   16.71    None  None   None       |
|    Sol.    : 438    0      4.38    94.36   41.29    None  None   None       |
|    Mac.    : 2385   0      0.00    97.63   12.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.763: 1210   |   5:    48.814 -  58.577:   94        |
|      1:     9.763 -  19.526:  946   |   6:    58.577 -  68.339:   56        |
|      2:    19.526 -  29.288:  227   |   7:    68.339 -  78.102:   28        |
|      3:    29.288 -  39.051:  133   |   8:    78.102 -  87.865:   12        |
|      4:    39.051 -  48.814:  114   |   9:    87.865 -  97.628:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.1890             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1444 r_free = 0.1890             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1890   ksol= 0.33   Bsol= 74.79   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,1.20,0.03,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.357604                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1890   ksol= 0.33   Bsol= 74.72   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.22,0.06,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.357742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.201290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.601340              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.446  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7042 = 3.20 * 0.50 * 5.3866 + 1.00 * 0.0822                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5624 = 3.20 * 0.50 * 5.3025 + 1.00 * 0.0750                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2001 = 0.60 * 1.00 * 5.3025 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1712 = 0.60 * 1.00 * 5.2485 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.04  16.43    None  None   None       |
|    all(noH): 2823   0      0.00    102.04  16.43    None  None   None       |
|    Sol.    : 438    0      4.37    101.23  41.86    None  None   None       |
|    Mac.    : 2385   0      0.00    102.04  11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.204: 1353   |   5:    51.019 -  61.223:   86        |
|      1:    10.204 -  20.408:  884   |   6:    61.223 -  71.427:   52        |
|      2:    20.408 -  30.611:  186   |   7:    71.427 -  81.630:   27        |
|      3:    30.611 -  40.815:  115   |   8:    81.630 -  91.834:    6        |
|      4:    40.815 -  51.019:  110   |   9:    91.834 - 102.038:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1238 r_free = 0.1739             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1740             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1740   ksol= 0.33   Bsol= 74.72   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,0.22,0.06,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.238269                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7989 0.99   1382  155 0.1005 0.1365      5.4198       5.601|
|  2:  4.7989 -  3.8294 0.99   1338  145 0.0883 0.1121      5.4728      5.6601|
|  3:  3.8294 -  3.3514 0.99   1307  150 0.1118 0.1609      5.5373      5.9032|
|  4:  3.3514 -  3.0477 0.99   1302  141 0.1357 0.1771      5.5449      5.7039|
|  5:  3.0477 -  2.8308 0.99   1284  142 0.1495 0.1875        5.45      5.6066|
|  6:  2.8308 -  2.6648 0.98   1290  143 0.1454 0.2255      5.3512      5.5871|
|  7:  2.6648 -  2.5320 0.99   1271  143 0.1407 0.1851       5.274      5.4614|
|  8:  2.5320 -  2.4222 0.98   1276  138 0.1347 0.1978      5.1985      5.4686|
|  9:  2.4222 -  2.3293 0.98   1282  145 0.1332 0.2004      5.1281      5.4386|
| 10:  2.3293 -  2.2492 0.98   1237  138 0.1307 0.1848      5.0912      5.2607|
| 11:  2.2492 -  2.1791 0.99   1271  145 0.1301 0.2006      5.0313      5.3641|
| 12:  2.1791 -  2.1170 0.98   1276  133 0.1241 0.1833      4.9747       5.227|
| 13:  2.1170 -  2.0614 0.97   1237  143 0.1300 0.1832      4.8848      5.1027|
| 14:  2.0614 -  2.0112 0.68    877   98 0.1229 0.1974       4.774      5.0651|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7989  1382   155  0.93   9.92   0.96     0.93       8206.91|
|  2:  4.7989 -  3.8294  1338   145  0.95   8.83   1.00     0.98      10076.08|
|  3:  3.8294 -  3.3514  1307   150  0.93  12.24   1.02     1.01      11861.00|
|  4:  3.3514 -  3.0477  1302   141  0.90  15.42   1.00     0.98      12218.92|
|  5:  3.0477 -  2.8308  1284   142  0.88  18.20   1.00     0.97      10722.39|
|  6:  2.8308 -  2.6648  1290   143  0.88  18.32   0.98     0.94       9005.25|
|  7:  2.6648 -  2.5320  1271   143  0.89  17.75   0.99     0.96       7785.29|
|  8:  2.5320 -  2.4222  1276   138  0.89  17.42   0.99     0.95       6900.01|
|  9:  2.4222 -  2.3293  1282   145  0.89  17.98   0.98     0.93       6003.15|
| 10:  2.3293 -  2.2492  1237   138  0.88  17.77   0.98     0.94       5635.35|
| 11:  2.2492 -  2.1791  1271   145  0.88  18.08   0.98     0.93       5121.72|
| 12:  2.1791 -  2.1170  1276   133  0.90  16.74   0.99     0.97       4733.77|
| 13:  2.1170 -  2.0614  1237   143  0.89  17.72   0.98     0.96       3968.19|
| 14:  2.0614 -  2.0112   877    98  0.89  16.89   0.95     0.91       3122.85|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3122.85 max =        12218.92 mean =      7667.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.85|
|phase err.(test): min =        0.00 max =           89.34 mean =        15.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1740   ksol= 0.32   Bsol= 71.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.02,0.22,0.00,0.00,0.00); trace/3= -0.26                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.238095                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1740   ksol= 0.32   Bsol= 71.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.02,0.22,0.00,0.00,0.00); trace/3= -0.26                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.238095                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7989 0.99   1382  155 0.1003 0.1366      5.4187      5.6007|
|  2:  4.7989 -  3.8294 0.99   1338  145 0.0883 0.1120      5.4723       5.659|
|  3:  3.8294 -  3.3514 0.99   1307  150 0.1119 0.1609      5.5375      5.9039|
|  4:  3.3514 -  3.0477 0.99   1302  141 0.1357 0.1772      5.5453      5.7038|
|  5:  3.0477 -  2.8308 0.99   1284  142 0.1495 0.1878      5.4501      5.6073|
|  6:  2.8308 -  2.6648 0.98   1290  143 0.1454 0.2249      5.3508      5.5849|
|  7:  2.6648 -  2.5320 0.99   1271  143 0.1407 0.1858      5.2738      5.4619|
|  8:  2.5320 -  2.4222 0.98   1276  138 0.1345 0.1981      5.1988      5.4691|
|  9:  2.4222 -  2.3293 0.98   1282  145 0.1331 0.2003      5.1282      5.4383|
| 10:  2.3293 -  2.2492 0.98   1237  138 0.1306 0.1857      5.0914      5.2629|
| 11:  2.2492 -  2.1791 0.99   1271  145 0.1299 0.2004      5.0309      5.3627|
| 12:  2.1791 -  2.1170 0.98   1276  133 0.1238 0.1834      4.9744      5.2291|
| 13:  2.1170 -  2.0614 0.97   1237  143 0.1302 0.1831      4.8849      5.1031|
| 14:  2.0614 -  2.0112 0.68    877   98 0.1229 0.1967      4.7728      5.0623|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7989  1382   155  0.93   9.92   0.96     0.93       8198.65|
|  2:  4.7989 -  3.8294  1338   145  0.95   8.82   1.00     0.98      10061.85|
|  3:  3.8294 -  3.3514  1307   150  0.93  12.23   1.02     1.01      11857.27|
|  4:  3.3514 -  3.0477  1302   141  0.90  15.43   1.00     0.98      12229.83|
|  5:  3.0477 -  2.8308  1284   142  0.88  18.18   1.00     0.97      10705.01|
|  6:  2.8308 -  2.6648  1290   143  0.88  18.30   0.98     0.95       8993.63|
|  7:  2.6648 -  2.5320  1271   143  0.89  17.74   0.99     0.96       7779.39|
|  8:  2.5320 -  2.4222  1276   138  0.89  17.44   0.99     0.95       6911.30|
|  9:  2.4222 -  2.3293  1282   145  0.89  17.99   0.99     0.93       6014.00|
| 10:  2.3293 -  2.2492  1237   138  0.88  17.78   0.99     0.94       5640.57|
| 11:  2.2492 -  2.1791  1271   145  0.88  18.09   0.98     0.93       5125.31|
| 12:  2.1791 -  2.1170  1276   133  0.90  16.75   0.99     0.97       4739.31|
| 13:  2.1170 -  2.0614  1237   143  0.89  17.72   0.98     0.97       3964.45|
| 14:  2.0614 -  2.0112   877    98  0.89  16.86   0.96     0.92       3109.70|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3109.70 max =        12229.83 mean =      7665.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.85|
|phase err.(test): min =        0.00 max =           89.34 mean =        15.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.352)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.04  16.43    None  None   None       |
|    all(noH): 2823   0      0.00    102.04  16.43    None  None   None       |
|    Sol.    : 438    0      4.37    101.23  41.86    None  None   None       |
|    Mac.    : 2385   0      0.00    102.04  11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.207: 1353   |   5:    51.022 -  61.226:   86        |
|      1:    10.207 -  20.411:  884   |   6:    61.226 -  71.430:   52        |
|      2:    20.411 -  30.614:  186   |   7:    71.430 -  81.633:   27        |
|      3:    30.614 -  40.818:  115   |   8:    81.633 -  91.837:    6        |
|      4:    40.818 -  51.022:  110   |   9:    91.837 - 102.041:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 4.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 324
   mapped sites are within: 0.712 - 4.878

peak=   10.909 closest distance to " O  BHOH Z  74 " =    1.076
peak=    6.059 closest distance to " O   HOH Z 210 " =    1.508
peak=    5.760 closest distance to " O   HOH Z 111 " =    2.232
peak=    5.120 closest distance to " CB  SER A  63 " =    1.261
peak=    4.969 closest distance to " O   HOH Z 433 " =    1.771
peak=    4.899 closest distance to " CB  GLN A 223 " =    1.363
peak=    4.795 closest distance to " CG  PRO A  54 " =    1.331
peak=    4.729 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.725 closest distance to " O   PRO A 198 " =    1.578
peak=    4.656 closest distance to " CB  GLN A 183 " =    1.314
peak=    4.635 closest distance to " O   HOH Z  49 " =    1.070
peak=    4.546 closest distance to " CB  ARG A 190 " =    1.749
peak=    4.541 closest distance to " O   HOH Z 232 " =    2.429
peak=    4.513 closest distance to " CA  ALA A  51 " =    0.985
peak=    4.499 closest distance to " O   HOH Z 134 " =    1.917
peak=    4.452 closest distance to " O   HOH Z 209 " =    2.353
peak=    4.361 closest distance to " CB  GLU A 128 " =    1.138
peak=    4.330 closest distance to " O   HOH Z 234 " =    3.763
peak=    4.267 closest distance to " O   HOH Z 133 " =    2.303
peak=    4.249 closest distance to " O   HOH Z 412 " =    3.382
peak=    4.243 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.231 closest distance to " O   HOH Z 369 " =    2.159
peak=    4.217 closest distance to " CB  TRP A 266 " =    1.007
peak=    4.205 closest distance to " O   HOH Z 418 " =    2.015
peak=    4.200 closest distance to " O   HOH Z 298 " =    1.985
peak=    4.183 closest distance to " O   HOH Z 357 " =    2.218
peak=    4.181 closest distance to " CB  PRO A  54 " =    0.818
peak=    4.175 closest distance to " CZ  PHE A 218 " =    1.112
peak=    4.173 closest distance to " OD1 ASN A 301 " =    1.195
peak=    4.157 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.131 closest distance to " O   HOH Z  80 " =    2.073
peak=    4.118 closest distance to " NH2 ARG A 156 " =    1.201
peak=    4.104 closest distance to " O   HOH Z  95 " =    1.981
peak=    4.096 closest distance to " O   HOH Z 196 " =    1.873
peak=    4.090 closest distance to " CB  GLU A 277 " =    3.849
peak=    4.087 closest distance to " O   HOH Z  15 " =    2.127
peak=    4.077 closest distance to " O   ALA A 165 " =    1.387
peak=    4.075 closest distance to " CG  PRO A 280 " =    0.815
peak=    4.046 closest distance to " O   HOH Z 423 " =    1.800
peak=    4.043 closest distance to " O   HOH Z 406 " =    1.618
peak=    4.040 closest distance to " O   HOH Z 425 " =    1.582
peak=    4.008 closest distance to " CB  ARG A 275 " =    0.844
peak=    3.994 closest distance to " O   HOH Z 403 " =    1.863
peak=    3.989 closest distance to " O   HOH Z 176 " =    2.168
peak=    3.985 closest distance to " CD  LYS A 166 " =    1.434
peak=    3.980 closest distance to " CA  ALA A 160 " =    1.009
peak=    3.977 closest distance to " CB  LEU A 228 " =    1.101
peak=    3.957 closest distance to " O   GLN A  11 " =    1.005
peak=    3.950 closest distance to " CG2BVAL A  41 " =    0.943
peak=    3.948 closest distance to " CA  SER A  12 " =    1.598
peak=    3.931 closest distance to " CA  ARG A 195 " =    1.119
peak=    3.926 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.921 closest distance to " O   HOH Z  63 " =    1.943
peak=    3.919 closest distance to " CB  TYR A 169 " =    0.754
peak=    3.904 closest distance to " O   HOH Z  40 " =    1.853
peak=    3.899 closest distance to " O   HOH Z 214 " =    1.480
peak=    3.894 closest distance to " CG  ARG A  66 " =    2.691
peak=    3.863 closest distance to " NE2 GLN A  11 " =    1.055
peak=    3.845 closest distance to " O   HOH Z  47 " =    1.381
peak=    3.844 closest distance to " O   THR A 251 " =    1.298
peak=    3.836 closest distance to " CG1 ILE A  33 " =    1.209
peak=    3.830 closest distance to " CD1 LEU A 300 " =    1.166
peak=    3.827 closest distance to " O   HOH Z 362 " =    3.215
peak=    3.826 closest distance to " CB  ASN A 148 " =    1.397
peak=    3.826 closest distance to " O   HOH Z  20 " =    1.849
peak=    3.817 closest distance to " O   HOH Z  97 " =    2.017
peak=    3.815 closest distance to " O   HOH Z 174 " =    1.998
peak=    3.812 closest distance to " O   HOH Z 374 " =    2.702
peak=    3.807 closest distance to " O   ASN A  74 " =    1.547
peak=    3.805 closest distance to " O   HOH Z 154 " =    1.304
peak=    3.798 closest distance to " OE1 GLN A  11 " =    2.175
peak=    3.797 closest distance to " CB  VAL A 202 " =    1.472
peak=    3.791 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.791 closest distance to " CZ3 TRP A  85 " =    0.897
peak=    3.791 closest distance to " CA  ALA A  21 " =    1.393
peak=    3.790 closest distance to " CZ  PHE A  38 " =    1.288
peak=    3.779 closest distance to " CB  SER A  62 " =    0.929
peak=    3.768 closest distance to " O   HOH Z 245 " =    1.273
peak=    3.768 closest distance to " O   HOH Z 132 " =    2.835
peak=    3.766 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.759 closest distance to " O   HOH Z 394 " =    1.700
peak=    3.740 closest distance to " O   HOH Z 415 " =    1.123
peak=    3.738 closest distance to " O   HOH Z 377 " =    1.337
peak=    3.720 closest distance to " O   HOH Z  88 " =    1.756
peak=    3.715 closest distance to " O   HOH Z 146 " =    1.640
peak=    3.712 closest distance to " O   SER A  87 " =    2.290
peak=    3.707 closest distance to " O   HOH Z 428 " =    1.095
peak=    3.704 closest distance to " CG2 VAL A 197 " =    1.189
peak=    3.696 closest distance to " O   HOH Z 265 " =    1.998
peak=    3.689 closest distance to " O   HOH Z 189 " =    2.617
peak=    3.679 closest distance to " CG2 VAL A  78 " =    0.987
peak=    3.677 closest distance to " NE2 HIS A 115 " =    1.119
peak=    3.668 closest distance to " OG BSER A 164 " =    2.256
peak=    3.666 closest distance to " CB  SER A 141 " =    1.012
peak=    3.661 closest distance to " O   HOH Z 258 " =    2.194
peak=    3.660 closest distance to " O   HOH Z   7 " =    1.109
peak=    3.660 closest distance to " O   HOH Z 404 " =    1.651
peak=    3.654 closest distance to " O   HOH Z 284 " =    2.979
peak=    3.651 closest distance to " CB  ARG A  79 " =    1.400
peak=    3.649 closest distance to " C   ILE A 106 " =    1.832
peak=    3.647 closest distance to " CB  GLN A  88 " =    1.153
peak=    3.644 closest distance to " O   HOH Z 422 " =    0.944
peak=    3.640 closest distance to " CA  GLY A 196 " =    1.059
peak=    3.632 closest distance to " O   HOH Z 271 " =    2.636
peak=    3.628 closest distance to " CB  ASN A  39 " =    0.850
peak=    3.625 closest distance to " O   HOH Z  78 " =    2.362
peak=    3.624 closest distance to " N   SER A 164 " =    1.029
peak=    3.616 closest distance to " O   HOH Z  30 " =    1.779
peak=    3.615 closest distance to " N   CYS A 260 " =    0.838
peak=    3.615 closest distance to " O  BHOH Z 338 " =    2.464
peak=    3.615 closest distance to " CB  MET A 105 " =    1.168
peak=    3.614 closest distance to " N   ASN A  39 " =    1.297
peak=    3.609 closest distance to " CD  ARG A 269 " =    0.953
peak=    3.600 closest distance to " O   HOH Z 437 " =    1.600
peak=    3.597 closest distance to " O   HOH Z  21 " =    1.855
peak=    3.585 closest distance to " CA  ASP A 191 " =    0.886
peak=    3.582 closest distance to " O   HOH Z 118 " =    1.152
peak=    3.577 closest distance to " CB  GLU A 152 " =    1.129
peak=    3.574 closest distance to " O   HOH Z 431 " =    1.195
peak=    3.569 closest distance to " O   HOH Z  90 " =    3.517
peak=    3.564 closest distance to " O   HOH Z 346 " =    1.637
peak=    3.563 closest distance to " CA  ILE A 106 " =    0.800
peak=    3.560 closest distance to " CB  ARG A  79 " =    0.885
peak=    3.552 closest distance to " O   HOH Z 193 " =    2.038
peak=    3.544 closest distance to " CA  LEU A  83 " =    1.426
peak=    3.533 closest distance to " O   ALA A 158 " =    1.215
peak=    3.533 closest distance to " CA  LYS A 117 " =    1.365
peak=    3.526 closest distance to " CD  ARG A 159 " =    0.879
peak=    3.524 closest distance to " O   HOH Z 432 " =    1.888
peak=    3.521 closest distance to " O   HOH Z 368 " =    4.257
peak=    3.521 closest distance to " CA  ASN A 217 " =    1.322
peak=    3.517 closest distance to " CD2 LEU A 297 " =    0.980
peak=    3.516 closest distance to " CB  MET A  40 " =    0.863
peak=    3.513 closest distance to " CA  GLN A  88 " =    1.296
peak=    3.510 closest distance to " CZ3 TRP A 266 " =    1.063
peak=    3.509 closest distance to " CA  ALA A 295 " =    1.130
peak=    3.508 closest distance to " CG  GLU A  37 " =    0.986
peak=    3.493 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.491 closest distance to " CB  ALA A 256 " =    1.471
peak=    3.488 closest distance to " O   HOH Z 336 " =    1.674
peak=    3.482 closest distance to " O   HOH Z  22 " =    2.485
peak=    3.479 closest distance to " CE  LYS A  76 " =    0.813
peak=    3.471 closest distance to " O   HOH Z 126 " =    1.645
peak=    3.466 closest distance to " O   HOH Z 365 " =    2.934
peak=    3.461 closest distance to " O   HOH Z 371 " =    3.160
peak=    3.454 closest distance to " CG  GLN A  77 " =    0.888
peak=    3.453 closest distance to " ND2 ASN A 301 " =    1.072
peak=    3.453 closest distance to " CD1 LEU A  96 " =    0.712
peak=    3.451 closest distance to " O   HOH Z 415 " =    1.712
peak=    3.445 closest distance to " O   HOH Z 395 " =    1.400
peak=    3.442 closest distance to " CA  ASN A 215 " =    1.103
peak=    3.436 closest distance to " CA  GLY A 241 " =    0.921
peak=    3.435 closest distance to " CB  ASP A 140 " =    0.786
peak=    3.434 closest distance to " O   ASP A 124 " =    1.307
peak=    3.433 closest distance to " CB  ALA A 100 " =    1.458
peak=    3.431 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.429 closest distance to " C   VAL A 265 " =    1.105
peak=    3.426 closest distance to " CB  ASN A 285 " =    0.789
peak=    3.425 closest distance to " CE1 HIS A 108 " =    1.127
peak=    3.421 closest distance to " O   HOH Z  48 " =    1.954
peak=    3.421 closest distance to " O   HOH Z 285 " =    3.230
peak=    3.418 closest distance to " CB  PHE A 283 " =    0.824
peak=    3.416 closest distance to " O   HOH Z 139 " =    4.757
peak=    3.415 closest distance to " O   HOH Z 189 " =    2.974
peak=    3.415 closest distance to " O   HOH Z 417 " =    3.096
peak=    3.412 closest distance to " N   TYR A 116 " =    1.544
peak=    3.412 closest distance to " CB  TYR A 116 " =    1.225
peak=    3.411 closest distance to " CA  VAL A 125 " =    1.287
peak=    3.411 closest distance to " O   HOH Z 423 " =    3.355
peak=    3.407 closest distance to " O   HOH Z 185 " =    1.740
peak=    3.407 closest distance to " CG AARG A 275 " =    1.161
peak=    3.407 closest distance to " O   HOH Z 120 " =    0.988
peak=    3.406 closest distance to " O   HOH Z 327 " =    1.700
peak=    3.406 closest distance to " CE1 TYR A 186 " =    1.240
peak=    3.406 closest distance to " CB  PRO A  54 " =    1.367
peak=    3.404 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.402 closest distance to " O   HOH Z 343 " =    2.397
peak=    3.402 closest distance to " OE1 GLN A  58 " =    3.434
peak=    3.401 closest distance to " CB  GLU A  46 " =    1.033
peak=    3.399 closest distance to " O   HOH Z 301 " =    1.497
peak=    3.396 closest distance to " CG1 VAL A 153 " =    1.100
peak=    3.395 closest distance to " O   HOH Z 389 " =    2.047
peak=    3.394 closest distance to " O   HOH Z 291 " =    1.388
peak=    3.393 closest distance to " O   HOH Z 316 " =    3.118
peak=    3.388 closest distance to " CG  PRO A 243 " =    1.166
peak=    3.388 closest distance to " CB  GLU A  37 " =    0.833
peak=    3.387 closest distance to " CA  ASN A 176 " =    1.316
peak=    3.386 closest distance to " O   HOH Z  11 " =    1.328
peak=    3.386 closest distance to " O   HOH Z 214 " =    2.730
peak=    3.384 closest distance to " O   HOH Z  44 " =    1.853
peak=    3.382 closest distance to " NE2 GLN A  77 " =    3.172
peak=    3.380 closest distance to " O  BHOH Z 338 " =    0.899
peak=    3.379 closest distance to " O   HOH Z 368 " =    2.215
peak=    3.372 closest distance to " O   HOH Z 344 " =    3.283
peak=    3.369 closest distance to " O   HOH Z 281 " =    4.878
peak=    3.366 closest distance to " CD  PRO A  54 " =    1.015
peak=    3.356 closest distance to " CG2 VAL A 126 " =    0.860
peak=    3.355 closest distance to " OE1 GLU A   2 " =    1.400
peak=    3.353 closest distance to " CG2 THR A  42 " =    0.904
peak=    3.349 closest distance to " O   HOH Z  68 " =    2.107
peak=    3.348 closest distance to " CB  GLU A 277 " =    0.835
peak=    3.345 closest distance to " OD2 ASP A 298 " =    3.686
peak=    3.342 closest distance to " NZ  LYS A 117 " =    2.829
peak=    3.339 closest distance to " CB  LEU A  83 " =    0.807
peak=    3.337 closest distance to " CB  ASN A 142 " =    1.203
peak=    3.337 closest distance to " CG2 ILE A  20 " =    1.389
peak=    3.333 closest distance to " O   HOH Z 383 " =    2.150
peak=    3.331 closest distance to " O   HOH Z 201 " =    2.873
peak=    3.329 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.328 closest distance to " O   HOH Z 303 " =    2.337
peak=    3.327 closest distance to " NH2BARG A 145 " =    1.988
peak=    3.322 closest distance to " O   HOH Z 373 " =    1.616
peak=    3.322 closest distance to " OG  SER A 245 " =    1.594
peak=    3.321 closest distance to " CA  THR A 221 " =    1.648
peak=    3.320 closest distance to " CA  ASP A 162 " =    1.155
peak=    3.315 closest distance to " O   HOH Z 227 " =    1.731
peak=    3.311 closest distance to " O   HOH Z 128 " =    2.055
peak=    3.311 closest distance to " O   HOH Z 435 " =    1.709
peak=    3.309 closest distance to " CB  ALA A 291 " =    1.204
peak=    3.308 closest distance to " O   GLY A  91 " =    1.091
peak=    3.307 closest distance to " CG ALYS A 290 " =    1.100
peak=    3.305 closest distance to " OG1 THR A 294 " =    2.460
peak=    3.299 closest distance to " CG2 THR A  29 " =    1.436
peak=    3.298 closest distance to " O   HOH Z 147 " =    1.654
peak=    3.298 closest distance to " O   HOH Z   6 " =    1.090
peak=    3.295 closest distance to " N   ILE A  33 " =    1.024
peak=    3.292 closest distance to " O   HOH Z 358 " =    1.420
peak=    3.290 closest distance to " O   HOH Z 394 " =    4.081
peak=    3.284 closest distance to " CG2 THR A 220 " =    0.774
peak=    3.281 closest distance to " O   HOH Z 145 " =    2.381
peak=    3.273 closest distance to " O   HOH Z 193 " =    1.749
peak=    3.273 closest distance to " CD  ARG A 195 " =    1.048
peak=    3.272 closest distance to " CA  ALA A 158 " =    1.203
peak=    3.270 closest distance to " OD1 ASN A  69 " =    2.533
peak=    3.268 closest distance to " CD  GLN A 194 " =    1.649
peak=    3.267 closest distance to " CB  ALA A  34 " =    0.730
peak=    3.266 closest distance to " O   HOH Z 405 " =    4.337
peak=    3.262 closest distance to " O   HOH Z 109 " =    2.172
peak=    3.259 closest distance to " CH2 TRP A 274 " =    2.011
peak=    3.259 closest distance to " N   GLY A  98 " =    1.022
peak=    3.257 closest distance to " CB  PRO A 243 " =    1.175
peak=    3.255 closest distance to " O   HOH Z 435 " =    2.958
peak=    3.252 closest distance to " CB  SER A  97 " =    1.180
peak=    3.249 closest distance to " NZ  LYS A 117 " =    2.228
peak=    3.249 closest distance to " O   HOH Z 135 " =    2.154
peak=    3.248 closest distance to " O   HOH Z 386 " =    2.305
peak=    3.248 closest distance to " CD ALYS A 290 " =    1.044
peak=    3.248 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.245 closest distance to " O   HOH Z 414 " =    1.640
peak=    3.244 closest distance to " CB  PRO A  90 " =    1.298
peak=    3.243 closest distance to " CG  ARG A 219 " =    1.248
peak=    3.242 closest distance to " O   HOH Z 134 " =    2.348
peak=    3.242 closest distance to " O   HOH Z  88 " =    3.572
peak=    3.240 closest distance to " OG  SER A  97 " =    3.555
peak=    3.240 closest distance to " O   HOH Z 426 " =    1.279
peak=    3.236 closest distance to " O   HOH Z 247 " =    1.538
peak=    3.232 closest distance to " O   ASP A 200 " =    1.609
peak=    3.231 closest distance to " O   HOH Z 279 " =    2.198
peak=    3.229 closest distance to " ND2 ASN A 187 " =    1.497
peak=    3.226 closest distance to " CD2 LEU A 255 " =    1.488
peak=    3.225 closest distance to " O   HOH Z 261 " =    1.841
peak=    3.222 closest distance to " O   HOH Z 163 " =    1.718
peak=    3.221 closest distance to " O   HOH Z 427 " =    3.319
peak=    3.217 closest distance to " CB  SER A   3 " =    1.388
peak=    3.217 closest distance to " C   GLY A  80 " =    1.049
peak=    3.211 closest distance to " CE3 TRP A  85 " =    1.167
peak=    3.211 closest distance to " O   HOH Z 380 " =    1.931
peak=    3.206 closest distance to " O   HOH Z 433 " =    1.994
peak=    3.205 closest distance to " CA  TRP A 274 " =    0.909
peak=    3.202 closest distance to " O   HOH Z 244 " =    1.701
peak=    3.201 closest distance to " O   HOH Z 301 " =    2.067
peak=    3.200 closest distance to " N   TYR A  15 " =    0.801
peak=    3.199 closest distance to " O   GLY A  57 " =    2.700
peak=    3.189 closest distance to " CA  SER A  32 " =    1.655
peak=    3.187 closest distance to " CA  THR A 246 " =    0.994
peak=    3.186 closest distance to " CA  SER A  87 " =    1.031
peak=    3.185 closest distance to " O   HOH Z 282 " =    2.050
peak=    3.185 closest distance to " O   HOH Z 150 " =    1.904
peak=    3.182 closest distance to " NH1 ARG A  14 " =    1.226
peak=    3.182 closest distance to " OG  SER A  62 " =    2.989
peak=    3.177 closest distance to " CA  GLU A  46 " =    0.914
peak=    3.175 closest distance to " O   HOH Z 294 " =    1.564
peak=    3.168 closest distance to " O   HOH Z 146 " =    1.327
peak=    3.167 closest distance to " CA  GLN A 223 " =    0.796
peak=    3.166 closest distance to " O   HOH Z  99 " =    2.471
peak=    3.163 closest distance to " CA  GLU A 152 " =    0.933
peak=    3.163 closest distance to " CD  LYS A 119 " =    1.798
peak=    3.163 closest distance to " OG1 THR A 294 " =    3.715
peak=    3.163 closest distance to " NZ  LYS A 193 " =    1.412
peak=    3.162 closest distance to " CA  ALA A 291 " =    0.899
peak=    3.162 closest distance to " CB  GLN A 103 " =    0.864
peak=    3.160 closest distance to " CB  PRO A 198 " =    0.902
peak=    3.157 closest distance to " O   HOH Z 353 " =    2.858
peak=    3.155 closest distance to " OH  TYR A 116 " =    1.321
peak=    3.151 closest distance to " CB  ILE A 120 " =    1.445
peak=    3.146 closest distance to " CG1BVAL A  72 " =    1.873
peak=    3.144 closest distance to " N   ASP A 132 " =    1.252
peak=    3.141 closest distance to " O   HOH Z 409 " =    3.126
peak=    3.136 closest distance to " CA  GLN A  11 " =    1.312
peak=    3.135 closest distance to " CG2 VAL A 257 " =    0.819
peak=    3.126 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.125 closest distance to " CA  ASP A 149 " =    1.214
peak=    3.122 closest distance to " O   TYR A 116 " =    1.435
peak=    3.114 closest distance to " O   HOH Z 199 " =    1.629
peak=    3.108 closest distance to " O   HOH Z 128 " =    1.790
peak=    3.100 closest distance to " O   HOH Z 141 " =    1.639
peak=    3.097 closest distance to " O   HOH Z 421 " =    1.904
peak=    3.096 closest distance to " CB  PHE A  16 " =    1.187
peak=    3.095 closest distance to " CD  PRO A 280 " =    0.998
peak=    3.092 closest distance to " O   HOH Z  48 " =    1.399
peak=    3.088 closest distance to " CG  LYS A  76 " =    1.153
peak=    3.073 closest distance to " NH2BARG A 145 " =    1.069
peak=    3.065 closest distance to " CA  ARG A 156 " =    1.097
peak=    3.058 closest distance to " O   HOH Z  50 " =    3.511
peak=    3.053 closest distance to " CB  PHE A  61 " =    0.727
peak=    3.051 closest distance to " O   HOH Z   2 " =    1.629
peak=    3.044 closest distance to " O   HOH Z 271 " =    2.077
peak=    3.038 closest distance to " O   SER A 273 " =    1.807
peak=    3.035 closest distance to " CB  PRO A 280 " =    1.151
peak=    3.030 closest distance to " CB  LEU A   5 " =    1.159

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 230         
Filter by distance & map next to the model:
   mapped sites are within: 0.740 - 5.268
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 229 from: 230
   mapped sites are within: 0.740 - 5.268

peak=   -4.521 closest distance to " O   HOH Z 166 " =    1.598
peak=   -4.505 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -4.441 closest distance to " CD  GLN A 223 " =    1.490
peak=   -4.437 closest distance to " O   HOH Z 266 " =    5.268
peak=   -4.347 closest distance to " CD  GLN A  58 " =    0.896
peak=   -4.298 closest distance to " O   VAL A  67 " =    2.948
peak=   -4.219 closest distance to " O   HOH Z 150 " =    0.858
peak=   -4.217 closest distance to " CD  GLN A  88 " =    0.916
peak=   -4.203 closest distance to " CD2 LEU A 237 " =    2.635
peak=   -4.197 closest distance to " O   HOH Z  19 " =    2.183
peak=   -4.063 closest distance to " O   PRO A 198 " =    1.331
peak=   -4.023 closest distance to " CG1 VAL A 112 " =    2.566
peak=   -4.007 closest distance to " CB  SER A 146 " =    2.219
peak=   -4.000 closest distance to " C   ASN A 285 " =    2.459
peak=   -3.997 closest distance to " CB  PRO A 243 " =    2.776
peak=   -3.969 closest distance to " OXT GLY A 302 " =    3.122
peak=   -3.947 closest distance to " CD  ARG A 156 " =    2.035
peak=   -3.938 closest distance to " OE1 GLN A  88 " =    0.888
peak=   -3.917 closest distance to " O   HOH Z 407 " =    0.740
peak=   -3.907 closest distance to " CE2 TYR A  30 " =    2.663
peak=   -3.892 closest distance to " NH2 ARG A  66 " =    1.588
peak=   -3.889 closest distance to " CD  PRO A 213 " =    2.283
peak=   -3.860 closest distance to " O   HOH Z 377 " =    0.865
peak=   -3.849 closest distance to " O   HOH Z 166 " =    2.357
peak=   -3.849 closest distance to " NE2 GLN A 223 " =    1.086
peak=   -3.845 closest distance to " O   HOH Z  58 " =    1.062
peak=   -3.844 closest distance to " O   HOH Z 155 " =    1.709
peak=   -3.838 closest distance to " ND2 ASN A  45 " =    1.762
peak=   -3.838 closest distance to " CD1 LEU A 167 " =    2.118
peak=   -3.828 closest distance to " O   HOH Z   7 " =    1.162
peak=   -3.826 closest distance to " O   VAL A  67 " =    3.029
peak=   -3.822 closest distance to " OE1 GLN A 223 " =    2.456
peak=   -3.799 closest distance to " CA  GLY A 203 " =    2.264
peak=   -3.795 closest distance to " SG  CYS A 254 " =    3.534
peak=   -3.770 closest distance to " CB  GLU A 277 " =    1.248
peak=   -3.766 closest distance to " O   GLN A  11 " =    1.135
peak=   -3.765 closest distance to " N   ALA A  43 " =    2.739
peak=   -3.752 closest distance to " O   HOH Z   6 " =    1.424
peak=   -3.750 closest distance to " CE2 PHE A  61 " =    2.634
peak=   -3.750 closest distance to " OD1 ASN A 148 " =    1.528
peak=   -3.749 closest distance to " C   HIS A 108 " =    1.093
peak=   -3.739 closest distance to " O   HOH Z   5 " =    1.608
peak=   -3.737 closest distance to " OG BSER A 210 " =    1.197
peak=   -3.733 closest distance to " O   HOH Z  15 " =    1.537
peak=   -3.719 closest distance to " O   HOH Z 369 " =    2.429
peak=   -3.695 closest distance to " O   HOH Z 348 " =    2.317
peak=   -3.685 closest distance to " OG  SER A  97 " =    2.242
peak=   -3.682 closest distance to " O   ILE A 109 " =    2.698
peak=   -3.672 closest distance to " C   THR A 279 " =    1.146
peak=   -3.665 closest distance to " CB  ALA A 131 " =    2.441
peak=   -3.643 closest distance to " CB  ALA A  10 " =    2.102
peak=   -3.635 closest distance to " O   HOH Z 275 " =    1.598
peak=   -3.611 closest distance to " O   HOH Z 109 " =    3.240
peak=   -3.609 closest distance to " NH2 ARG A 159 " =    2.438
peak=   -3.607 closest distance to " CD2 PHE A  61 " =    1.998
peak=   -3.607 closest distance to " CG  PRO A 243 " =    1.682
peak=   -3.606 closest distance to " CD2 PHE A 225 " =    1.302
peak=   -3.605 closest distance to " CB  ALA A  43 " =    2.637
peak=   -3.591 closest distance to " CG  ARG A 269 " =    2.373
peak=   -3.586 closest distance to " O   HOH Z 290 " =    1.161
peak=   -3.579 closest distance to " CH2 TRP A 179 " =    1.272
peak=   -3.574 closest distance to " O   ALA A  34 " =    2.454
peak=   -3.573 closest distance to " O   HOH Z 198 " =    2.535
peak=   -3.567 closest distance to " O   HOH Z 234 " =    4.314
peak=   -3.567 closest distance to " O   SER A 276 " =    1.767
peak=   -3.561 closest distance to " O   HOH Z 109 " =    3.620
peak=   -3.551 closest distance to " NE2 GLN A 194 " =    2.026
peak=   -3.516 closest distance to " O   HOH Z 394 " =    1.672
peak=   -3.515 closest distance to " NE2 GLN A  94 " =    1.694
peak=   -3.514 closest distance to " CD1 PHE A 130 " =    2.396
peak=   -3.513 closest distance to " O   HOH Z 418 " =    1.304
peak=   -3.512 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.512 closest distance to " CG  MET A  93 " =    2.539
peak=   -3.507 closest distance to " OD1 ASP A 191 " =    1.749
peak=   -3.504 closest distance to " O   HOH Z 308 " =    1.617
peak=   -3.499 closest distance to " O   HOH Z  49 " =    0.996
peak=   -3.498 closest distance to " O   HOH Z 200 " =    1.242
peak=   -3.497 closest distance to " CG  GLN A  11 " =    1.296
peak=   -3.495 closest distance to " CB  ASP A 132 " =    2.411
peak=   -3.494 closest distance to " O   HOH Z 292 " =    4.636
peak=   -3.483 closest distance to " O   HOH Z 117 " =    4.521
peak=   -3.482 closest distance to " O   HOH Z 422 " =    1.133
peak=   -3.480 closest distance to " ND2 ASN A  60 " =    1.603
peak=   -3.479 closest distance to " O   TRP A  92 " =    1.985
peak=   -3.471 closest distance to " O   PHE A 218 " =    1.416
peak=   -3.467 closest distance to " CA  VAL A 197 " =    0.981
peak=   -3.465 closest distance to " O   HOH Z 185 " =    2.276
peak=   -3.459 closest distance to " O   SER A 210 " =    1.965
peak=   -3.458 closest distance to " O   SER A 206 " =    1.447
peak=   -3.452 closest distance to " O   GLY A  75 " =    2.029
peak=   -3.452 closest distance to " O   HOH Z 388 " =    1.924
peak=   -3.447 closest distance to " O   HOH Z 351 " =    1.565
peak=   -3.446 closest distance to " CG2 VAL A 189 " =    2.283
peak=   -3.445 closest distance to " O   HOH Z 207 " =    1.622
peak=   -3.441 closest distance to " O   ASP A 171 " =    1.013
peak=   -3.438 closest distance to " O   HOH Z 251 " =    5.048
peak=   -3.438 closest distance to " O   HOH Z 422 " =    1.701
peak=   -3.433 closest distance to " CA  PRO A 198 " =    1.195
peak=   -3.431 closest distance to " CG2 ILE A  49 " =    2.656
peak=   -3.430 closest distance to " OG BSER A 210 " =    2.321
peak=   -3.429 closest distance to " O   HOH Z  90 " =    1.934
peak=   -3.427 closest distance to " CA  SER A 276 " =    1.439
peak=   -3.413 closest distance to " CB  ALA A 291 " =    2.444
peak=   -3.413 closest distance to " N   ARG A 275 " =    0.991
peak=   -3.413 closest distance to " OG1 THR A  82 " =    1.756
peak=   -3.405 closest distance to " O   PRO A 163 " =    2.241
peak=   -3.402 closest distance to " O   HOH Z 111 " =    1.410
peak=   -3.400 closest distance to " O   HOH Z  71 " =    1.816
peak=   -3.398 closest distance to " OD2 ASP A 171 " =    1.917
peak=   -3.396 closest distance to " CB  PHE A 192 " =    2.065
peak=   -3.396 closest distance to " O   HOH Z 283 " =    2.190
peak=   -3.395 closest distance to " CG  GLU A  53 " =    1.400
peak=   -3.393 closest distance to " O   HOH Z 189 " =    1.761
peak=   -3.389 closest distance to " OG  SER A  87 " =    1.729
peak=   -3.378 closest distance to " O   ARG A  79 " =    1.050
peak=   -3.375 closest distance to " O   HOH Z 137 " =    1.392
peak=   -3.372 closest distance to " O   HOH Z 423 " =    2.385
peak=   -3.372 closest distance to " CD2 PHE A  59 " =    2.435
peak=   -3.368 closest distance to " O   HOH Z 366 " =    1.934
peak=   -3.368 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.363 closest distance to " O   HOH Z 392 " =    1.251
peak=   -3.360 closest distance to " O   HOH Z  90 " =    3.759
peak=   -3.359 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.353 closest distance to " N   GLN A  58 " =    1.422
peak=   -3.351 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.347 closest distance to " CG2BVAL A  41 " =    1.551
peak=   -3.341 closest distance to " CD  ARG A 139 " =    1.504
peak=   -3.341 closest distance to " O   HOH Z  37 " =    1.884
peak=   -3.340 closest distance to " O   HOH Z  52 " =    2.013
peak=   -3.337 closest distance to " O   HOH Z 171 " =    2.355
peak=   -3.334 closest distance to " O   HOH Z 184 " =    1.478
peak=   -3.333 closest distance to " CB  PRO A 280 " =    2.280
peak=   -3.330 closest distance to " O   HOH Z  43 " =    1.241
peak=   -3.327 closest distance to " O   HOH Z  40 " =    2.870
peak=   -3.324 closest distance to " CD2 HIS A 115 " =    1.096
peak=   -3.323 closest distance to " O   ALA A   1 " =    2.065
peak=   -3.319 closest distance to " CD1 ILE A 263 " =    2.038
peak=   -3.316 closest distance to " O   HOH Z 197 " =    1.941
peak=   -3.314 closest distance to " O   HOH Z 149 " =    1.819
peak=   -3.313 closest distance to " O   HOH Z 313 " =    1.382
peak=   -3.312 closest distance to " O   HOH Z 422 " =    1.310
peak=   -3.311 closest distance to " C   ARG A  79 " =    2.699
peak=   -3.309 closest distance to " O   HOH Z 150 " =    1.831
peak=   -3.302 closest distance to " O   HOH Z 128 " =    2.537
peak=   -3.302 closest distance to " ND2 ASN A  45 " =    1.148
peak=   -3.300 closest distance to " O   HOH Z 134 " =    2.183
peak=   -3.295 closest distance to " O   HOH Z 196 " =    2.176
peak=   -3.289 closest distance to " O   VAL A 174 " =    2.049
peak=   -3.283 closest distance to " O   VAL A 189 " =    2.568
peak=   -3.280 closest distance to " O   HOH Z 236 " =    1.850
peak=   -3.279 closest distance to " O   HOH Z 252 " =    4.036
peak=   -3.279 closest distance to " C   TRP A 274 " =    1.281
peak=   -3.277 closest distance to " N   ASP A 272 " =    1.225
peak=   -3.277 closest distance to " O   LEU A 101 " =    2.167
peak=   -3.274 closest distance to " CH2 TRP A 177 " =    2.040
peak=   -3.268 closest distance to " OD1 ASP A 298 " =    2.014
peak=   -3.260 closest distance to " O   HOH Z 426 " =    1.734
peak=   -3.259 closest distance to " OE2 GLU A  53 " =    1.130
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.369
peak=   -3.253 closest distance to " O   HOH Z  93 " =    2.309
peak=   -3.252 closest distance to " O   HOH Z 113 " =    2.376
peak=   -3.250 closest distance to " O   HOH Z 133 " =    1.601
peak=   -3.250 closest distance to " O   HOH Z 424 " =    2.991
peak=   -3.249 closest distance to " O   HOH Z 326 " =    4.950
peak=   -3.249 closest distance to " O   GLY A 118 " =    2.319
peak=   -3.248 closest distance to " OG  SER A  26 " =    1.521
peak=   -3.248 closest distance to " NE2 GLN A 103 " =    1.817
peak=   -3.247 closest distance to " CG1 VAL A 197 " =    2.343
peak=   -3.243 closest distance to " O   HOH Z 128 " =    4.369
peak=   -3.242 closest distance to " O   HOH Z 165 " =    1.922
peak=   -3.238 closest distance to " CZ  PHE A  38 " =    2.037
peak=   -3.236 closest distance to " OD1 ASN A 301 " =    0.912
peak=   -3.234 closest distance to " SG  CYS A 168 " =    1.198
peak=   -3.232 closest distance to " CB  PHE A  16 " =    2.418
peak=   -3.227 closest distance to " ND2 ASN A 249 " =    2.319
peak=   -3.226 closest distance to " O   HOH Z 331 " =    1.247
peak=   -3.220 closest distance to " ND2 ASN A  60 " =    1.870
peak=   -3.220 closest distance to " CG1 VAL A  78 " =    2.743
peak=   -3.220 closest distance to " N   SER A 134 " =    1.273
peak=   -3.215 closest distance to " CE  MET A 105 " =    2.220
peak=   -3.215 closest distance to " O   HOH Z 298 " =    2.861
peak=   -3.212 closest distance to " O   HOH Z   7 " =    1.641
peak=   -3.212 closest distance to " O   ALA A  10 " =    1.885
peak=   -3.210 closest distance to " CG  MET A 105 " =    0.909
peak=   -3.205 closest distance to " O   ALA A  34 " =    2.039
peak=   -3.193 closest distance to " O  BHOH Z  74 " =    1.157
peak=   -3.192 closest distance to " CB  ALA A 100 " =    1.958
peak=   -3.192 closest distance to " O   HOH Z  88 " =    2.496
peak=   -3.188 closest distance to " CZ  PHE A  38 " =    2.466
peak=   -3.185 closest distance to " O   HOH Z 393 " =    1.675
peak=   -3.184 closest distance to " CG  PRO A 163 " =    1.711
peak=   -3.181 closest distance to " CE  MET A  93 " =    1.901
peak=   -3.178 closest distance to " O  BHOH Z 338 " =    1.408
peak=   -3.177 closest distance to " O   HOH Z  91 " =    2.249
peak=   -3.177 closest distance to " CG  ASP A 231 " =    0.835
peak=   -3.175 closest distance to " OD2 ASP A 298 " =    1.020
peak=   -3.174 closest distance to " CG2 THR A 221 " =    2.393
peak=   -3.173 closest distance to " O   HOH Z 259 " =    1.984
peak=   -3.173 closest distance to " CE  LYS A 119 " =    2.006
peak=   -3.172 closest distance to " O   HOH Z 241 " =    1.253
peak=   -3.163 closest distance to " CG2 ILE A 263 " =    2.255
peak=   -3.162 closest distance to " O   HOH Z 156 " =    3.641
peak=   -3.151 closest distance to " O   HOH Z  78 " =    1.835
peak=   -3.146 closest distance to " O   HOH Z 414 " =    1.481
peak=   -3.145 closest distance to " O   THR A  18 " =    1.622
peak=   -3.145 closest distance to " CG  LEU A  83 " =    2.144
peak=   -3.143 closest distance to " O   HOH Z 350 " =    1.149
peak=   -3.139 closest distance to " O   SER A 135 " =    1.773
peak=   -3.130 closest distance to " N   ALA A 226 " =    2.066
peak=   -3.125 closest distance to " OE1 GLN A  88 " =    1.363
peak=   -3.123 closest distance to " CA  GLY A 241 " =    3.332
peak=   -3.113 closest distance to " O   HOH Z 151 " =    1.516
peak=   -3.113 closest distance to " CB  ASP A 162 " =    2.468
peak=   -3.113 closest distance to " CD1 ILE A 106 " =    2.127
peak=   -3.111 closest distance to " O   HOH Z 318 " =    1.429
peak=   -3.109 closest distance to " CG  PRO A 163 " =    2.559
peak=   -3.109 closest distance to " O   HOH Z 174 " =    1.826
peak=   -3.105 closest distance to " CH2 TRP A 150 " =    1.107
peak=   -3.103 closest distance to " CB  ASP A 124 " =    2.335
peak=   -3.103 closest distance to " O   HOH Z 301 " =    2.455
peak=   -3.096 closest distance to " O   HOH Z  48 " =    0.829
peak=   -3.093 closest distance to " O   HOH Z 423 " =    1.350
peak=   -3.091 closest distance to " O   HOH Z 368 " =    1.984
peak=   -3.047 closest distance to " CD  GLN A  88 " =    0.893
peak=   -3.043 closest distance to " CB  ALA A   1 " =    1.277
peak=   -3.039 closest distance to " O   HOH Z 351 " =    1.375
peak=   -3.034 closest distance to " NE2 GLN A  58 " =    2.881
peak=   -3.021 closest distance to " C   GLU A  46 " =    1.061
peak=   -2.928 closest distance to " NH2 ARG A  66 " =    1.358

================= 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    :  0.4281 0.4085   6.246127e+00   6.207241e+00
   1_bss:  0.4172 0.3977   6.235094e+00   6.192885e+00
   1_xyz:  0.3485 0.3701   6.107233e+00   6.142523e+00
   1_adp:  0.3235 0.3775   6.062744e+00   6.149642e+00
   1_occ:  0.3230 0.3768   6.061802e+00   6.149023e+00
   2_bss:  0.3226 0.3763   6.063824e+00   6.150246e+00
   2_xyz:  0.2713 0.3174   5.915034e+00   6.034213e+00
   2_adp:  0.2573 0.3177   5.890965e+00   6.035973e+00
   2_occ:  0.2571 0.3177   5.890396e+00   6.035771e+00
   3_bss:  0.2570 0.3169   5.892484e+00   6.037557e+00
   3_xyz:  0.2196 0.2774   5.738369e+00   5.909568e+00
   3_adp:  0.2097 0.2607   5.695834e+00   5.859402e+00
   3_occ:  0.2095 0.2605   5.695158e+00   5.859038e+00
   4_bss:  0.2094 0.2600   5.695096e+00   5.857805e+00
   4_xyz:  0.1592 0.1988   5.432115e+00   5.621378e+00
   4_adp:  0.1446 0.1890   5.358243e+00   5.568112e+00
   4_occ:  0.1444 0.1890   5.357604e+00   5.567963e+00
   5_bss:  0.1447 0.1890   5.357742e+00   5.565945e+00
   5_xyz:  0.1278 0.1757   5.263088e+00   5.492259e+00
   5_adp:  0.1238 0.1739   5.238488e+00   5.473777e+00
   5_occ:  0.1238 0.1740   5.238269e+00   5.473702e+00
   5_bss:  0.1237 0.1740   5.238095e+00   5.473655e+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:  0.299  50.000  -2.638   5.565  -1.500   0.000  -0.000  -0.000
   1_xyz:  0.299  50.000  -2.638   5.565  -1.500   0.000  -0.000  -0.000
   1_adp:  0.299  50.000  -2.638   5.565  -1.500   0.000  -0.000  -0.000
   1_occ:  0.299  50.000  -2.638   5.565  -1.500   0.000  -0.000  -0.000
   2_bss:  0.300  50.000  -1.725   3.414  -0.576   0.000  -0.000  -0.000
   2_xyz:  0.300  50.000  -1.725   3.414  -0.576   0.000  -0.000  -0.000
   2_adp:  0.300  50.000  -1.725   3.414  -0.576   0.000  -0.000  -0.000
   2_occ:  0.300  50.000  -1.725   3.414  -0.576   0.000  -0.000  -0.000
   3_bss:  0.312  65.413  -0.816   2.565   0.230   0.000   0.000   0.000
   3_xyz:  0.312  65.413  -0.816   2.565   0.230   0.000   0.000   0.000
   3_adp:  0.312  65.413  -0.816   2.565   0.230   0.000   0.000   0.000
   3_occ:  0.312  65.413  -0.816   2.565   0.230   0.000   0.000   0.000
   4_bss:  0.325  74.794  -1.022   1.199   0.034   0.000   0.000   0.000
   4_xyz:  0.325  74.794  -1.022   1.199   0.034   0.000   0.000   0.000
   4_adp:  0.325  74.794  -1.022   1.199   0.034   0.000   0.000   0.000
   4_occ:  0.325  74.794  -1.022   1.199   0.034   0.000   0.000   0.000
   5_bss:  0.330  74.722  -1.153   0.217   0.060   0.000   0.000   0.000
   5_xyz:  0.330  74.722  -1.153   0.217   0.060   0.000   0.000   0.000
   5_adp:  0.330  74.722  -1.153   0.217   0.060   0.000   0.000   0.000
   5_occ:  0.330  74.722  -1.153   0.217   0.060   0.000   0.000   0.000
   5_bss:  0.324  71.802  -1.015   0.025   0.218   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.147 0.5709  0.7260    52068.622
   1_bss:  45.455 0.5779  0.7460    49082.372
   1_xyz:  41.997 0.6191  0.7895    41314.815
   1_adp:  42.464 0.6130  0.7740    41881.221
   1_occ:  42.481 0.6127  0.7728    41825.354
   2_bss:  42.299 0.6150  0.7761    41703.883
   2_xyz:  34.877 0.7022  0.8715    28970.152
   2_adp:  35.046 0.7001  0.8500    29099.663
   2_occ:  35.025 0.7004  0.8498    29073.100
   3_bss:  34.978 0.7011  0.8608    29155.449
   3_xyz:  28.847 0.7701  0.9299    20562.065
   3_adp:  26.489 0.7965  0.9379    18279.142
   3_occ:  26.459 0.7968  0.9381    18247.497
   4_bss:  26.356 0.7979  0.9211    18156.139
   4_xyz:  19.474 0.8663  0.9683    10230.245
   4_adp:  17.998 0.8804  0.9654     9201.799
   4_occ:  17.986 0.8805  0.9655     9199.447
   5_bss:  17.915 0.8811  0.9539     9119.957
   5_xyz:  16.260 0.8961  0.9629     7883.280
   5_adp:  15.795 0.9004  0.9562     7667.424
   5_occ:  15.791 0.9004  0.9562     7666.961
   5_bss:  15.788 0.9005  0.9577     7664.933
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6745e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6745e-01
   1_xyz:   1.313  0.010  0.081 15.382  0.005  4.113   9.6921e-02
   1_adp:   1.313  0.010  0.081 15.382  0.005  4.113   9.6921e-02
   1_occ:   1.313  0.010  0.081 15.382  0.005  4.113   9.6921e-02
   2_bss:   1.313  0.010  0.081 15.382  0.005  4.113   9.6921e-02
   2_xyz:   1.253  0.009  0.083 14.899  0.006  4.113   8.3854e-02
   2_adp:   1.253  0.009  0.083 14.899  0.006  4.113   8.3854e-02
   2_occ:   1.253  0.009  0.083 14.899  0.006  4.113   8.3854e-02
   3_bss:   1.253  0.009  0.083 14.899  0.006  4.113   8.3854e-02
   3_xyz:   1.063  0.007  0.068 14.602  0.004  4.123   6.4911e-02
   3_adp:   1.063  0.007  0.068 14.602  0.004  4.123   6.4911e-02
   3_occ:   1.063  0.007  0.068 14.602  0.004  4.123   6.4911e-02
   4_bss:   1.063  0.007  0.068 14.602  0.004  4.123   6.4911e-02
   4_xyz:   1.206  0.010  0.085 14.781  0.004  4.115   8.2177e-02
   4_adp:   1.206  0.010  0.085 14.781  0.004  4.115   8.2177e-02
   4_occ:   1.206  0.010  0.085 14.781  0.004  4.115   8.2177e-02
   5_bss:   1.206  0.010  0.085 14.781  0.004  4.115   8.2177e-02
   5_xyz:   1.114  0.010  0.081 14.828  0.004  4.125   7.4956e-02
   5_adp:   1.114  0.010  0.081 14.828  0.004  4.125   7.4956e-02
   5_occ:   1.114  0.010  0.081 14.828  0.004  4.125   7.4956e-02
   5_bss:   1.114  0.010  0.081 14.828  0.004  4.125   7.4956e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.545   2.4478e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.545   2.4478e-01
   1_xyz:   8.740  0.062  0.358 85.203  0.041  2.149   1.5267e-01
   1_adp:   8.740  0.062  0.358 85.203  0.041  2.149   1.5267e-01
   1_occ:   8.740  0.062  0.358 85.203  0.041  2.149   1.5267e-01
   2_bss:   8.740  0.062  0.358 85.203  0.041  2.149   1.5267e-01
   2_xyz:   7.073  0.042  0.240 85.391  0.022  2.256   8.7544e-02
   2_adp:   7.073  0.042  0.240 85.391  0.022  2.256   8.7544e-02
   2_occ:   7.073  0.042  0.240 85.391  0.022  2.256   8.7544e-02
   3_bss:   7.073  0.042  0.240 85.391  0.022  2.256   8.7544e-02
   3_xyz:   6.938  0.039  0.312 86.882  0.052  2.201   5.1552e-02
   3_adp:   6.938  0.039  0.312 86.882  0.052  2.201   5.1552e-02
   3_occ:   6.938  0.039  0.312 86.882  0.052  2.201   5.1552e-02
   4_bss:   6.938  0.039  0.312 86.882  0.052  2.201   5.1552e-02
   4_xyz:   8.063  0.066  0.260 83.288  0.038  2.166   5.2685e-02
   4_adp:   8.063  0.066  0.260 83.288  0.038  2.166   5.2685e-02
   4_occ:   8.063  0.066  0.260 83.288  0.038  2.166   5.2685e-02
   5_bss:   8.063  0.066  0.260 83.288  0.038  2.166   5.2685e-02
   5_xyz:   8.038  0.053  0.274 82.684  0.035  2.293   6.0449e-02
   5_adp:   8.038  0.053  0.274 82.684  0.035  2.293   6.0449e-02
   5_occ:   8.038  0.053  0.274 82.684  0.035  2.293   6.0449e-02
   5_bss:   8.038  0.053  0.274 82.684  0.035  2.293   6.0449e-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:  76.02   0.00  17.22  76.02   0.00  13.89  71.90   0.00  35.33
   1_occ:  76.02   0.00  17.22  76.02   0.00  13.89  71.90   0.00  35.33
   2_bss:  76.02   0.00  17.22  76.02   0.00  13.89  71.90   0.00  35.33
   2_xyz:  76.02   0.00  17.22  76.02   0.00  13.89  71.90   0.00  35.33
   2_adp:  94.60   0.00  18.12  94.60   0.00  14.46  87.28   0.18  38.03
   2_occ:  94.60   0.00  18.12  94.60   0.00  14.46  87.28   0.18  38.03
   3_bss:  94.60   0.00  18.12  94.60   0.00  14.46  87.28   0.18  38.03
   3_xyz:  94.60   0.00  18.12  94.60   0.00  14.46  87.28   0.18  38.03
   3_adp:  91.47   0.00  16.88  91.47   0.00  12.99  86.84   1.57  38.05
   3_occ:  91.47   0.00  16.88  91.47   0.00  12.99  86.84   1.57  38.05
   4_bss:  91.47   0.00  16.88  91.47   0.00  12.99  86.84   1.57  38.05
   4_xyz:  91.47   0.00  16.88  91.47   0.00  12.99  86.84   1.57  38.05
   4_adp:  97.63   0.00  16.71  97.63   0.00  12.20  94.36   4.38  41.29
   4_occ:  97.63   0.00  16.71  97.63   0.00  12.20  94.36   4.38  41.29
   5_bss:  97.63   0.00  16.71  97.63   0.00  12.20  94.36   4.38  41.29
   5_xyz:  97.63   0.00  16.71  97.63   0.00  12.20  94.36   4.38  41.29
   5_adp: 102.04   0.00  16.43 102.04   0.00  11.76 101.23   4.37  41.86
   5_occ: 102.04   0.00  16.43 102.04   0.00  11.76 101.23   4.37  41.86
   5_bss: 102.04   0.00  16.43 102.04   0.00  11.76 101.23   4.37  41.86
------------------------------------------------------------------------
 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:    1.550    0.024    0.276
   1_adp:    1.550    0.024    0.276
   1_occ:    1.550    0.024    0.276
   2_bss:    1.550    0.024    0.276
   2_xyz:    1.320    0.039    0.436
   2_adp:    1.320    0.039    0.436
   2_occ:    1.320    0.039    0.436
   3_bss:    1.320    0.039    0.436
   3_xyz:    1.423    0.024    0.589
   3_adp:    1.423    0.024    0.589
   3_occ:    1.423    0.024    0.589
   4_bss:    1.423    0.024    0.589
   4_xyz:    1.571    0.041    0.716
   4_adp:    1.571    0.041    0.716
   4_occ:    1.571    0.041    0.716
   5_bss:    1.571    0.041    0.716
   5_xyz:    1.582    0.091    0.762
   5_adp:    1.582    0.091    0.762
   5_occ:    1.582    0.091    0.762
   5_bss:    1.582    0.091    0.762
------------------------------------------------------------------------

CPU time actual refinement: 327.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/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_963/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_963/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.37 
  Macro-tasks:
    bulk solvent and scale       = 36.52  
    individual site refinement   = 138.50 
    weights calculation          = 28.63  
    collect and process          = 6.50   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.27 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 104.44 
    alpha_beta                      = 8.50   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 114.59 
    fmodel                         = 6.33   
    r_factors                      = 0.20   
    phase_errors                   = 10.81  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 248.67 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.642 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    644 calls, 104.00 s
gradients_fft:          589 calls, 101.23 s

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

# Date 2008-01-16 Time 06:05:11 PST -0800 (1200492311.74 s)
Start R-work = 0.4281, R-free = 0.4085 (no bulk solvent and anisotropic scale)
Final R-work = 0.1399, R-free = 0.1876 (no bulk solvent and anisotropic scale)

Start R-work = 0.4172, R-free = 0.3977
Final R-work = 0.1237, R-free = 0.1740