# Date 2008-01-16 Time 05:51:07 PST -0800 (1200491467.29 s)
#phil __OFF__

Command line arguments: "../902.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 939
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 902

-------------------------------------------------------------------------------
  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, 46.93, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95131
Completeness in resolution range: 0.930152
Completeness with d_max=infinity: 0.927378

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9513

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, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95131
Completeness in resolution range: 0.930152
Completeness with d_max=infinity: 0.927378

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1766 [2211/2240]  1992   219   9.9%
  bin  2:  4.1766 -  3.3270 [2114/2137]  1903   211  10.0%
  bin  3:  3.3270 -  2.9099 [2093/2115]  1877   216  10.3%
  bin  4:  2.9099 -  2.6454 [2082/2101]  1885   197   9.5%
  bin  5:  2.6454 -  2.4567 [2064/2093]  1849   215  10.4%
  bin  6:  2.4567 -  2.3124 [2040/2082]  1841   199   9.8%
  bin  7:  2.3124 -  2.1970 [2049/2085]  1843   206  10.1%
  bin  8:  2.1970 -  2.1016 [2009/2046]  1809   200  10.0%
  bin  9:  2.1016 -  2.0209 [2055/2087]  1850   205  10.0%
  bin 10:  2.0209 -  1.9513 [ 872/2074]   781    91  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 21
        2.20 -     2.88: 1286
        2.88 -     3.55: 4461
        3.55 -     4.23: 9299
        4.23 -     4.90: 13481
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.530 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.562 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.773 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  17 " - " O   HOH Z 333 "  1.891 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28543 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_902/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.93 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3804   r_free= 0.3840   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.170842                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6589 0.99   1428  159 0.3127 0.3136      6.4352      6.4318|
|  2:  4.6589 -  3.7164 0.99   1387  150 0.3094 0.2794      6.6042      6.5775|
|  3:  3.7164 -  3.2521 0.99   1357  156 0.3407 0.3589      6.4998        6.62|
|  4:  3.2521 -  2.9572 0.99   1343  148 0.3593 0.3667      6.3696      6.3866|
|  5:  2.9572 -  2.7467 0.99   1323  146 0.3938 0.3690      6.2382      6.2296|
|  6:  2.7467 -  2.5856 0.98   1326  152 0.4152 0.4051      6.1659      6.1306|
|  7:  2.5856 -  2.4567 0.99   1342  147 0.3981 0.3715      6.1327      6.0739|
|  8:  2.4567 -  2.3502 0.99   1312  145 0.4176 0.4198      6.0652      6.1044|
|  9:  2.3502 -  2.2600 0.98   1312  149 0.4183 0.4280      6.0372       5.995|
| 10:  2.2600 -  2.1823 0.98   1313  148 0.4289 0.4809      6.0133      6.0828|
| 11:  2.1823 -  2.1142 0.98   1317  138 0.4307 0.5196      5.9506      6.0361|
| 12:  2.1142 -  2.0539 0.99   1314  145 0.4347 0.4626       5.886      5.9277|
| 13:  2.0539 -  2.0000 0.90   1189  141 0.4549 0.4416      5.8291      5.7886|
| 14:  2.0000 -  1.9513 0.27    367   35 0.5333 0.5266      5.8125      5.7631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6589  1428   159  0.77  28.30   0.86     0.78      49135.74|
|  2:  4.6589 -  3.7164  1387   150  0.79  27.43   0.96     0.89      66845.29|
|  3:  3.7164 -  3.2521  1357   156  0.72  33.59   0.96     0.90      72260.16|
|  4:  3.2521 -  2.9572  1343   148  0.65  39.70   0.98     0.86      66578.23|
|  5:  2.9572 -  2.7467  1323   146  0.59  44.95   0.94     0.79      54520.91|
|  6:  2.7467 -  2.5856  1326   152  0.58  45.64   0.95     0.78      46699.88|
|  7:  2.5856 -  2.4567  1342   147  0.60  44.06   0.99     0.78      40816.24|
|  8:  2.4567 -  2.3502  1312   145  0.58  46.07   0.96     0.81      38468.25|
|  9:  2.3502 -  2.2600  1312   149  0.56  47.35   1.00     0.78      35888.55|
| 10:  2.2600 -  2.1823  1313   148  0.52  50.88   1.01     0.74      37877.58|
| 11:  2.1823 -  2.1142  1317   138  0.48  53.60   1.01     0.70      36054.03|
| 12:  2.1142 -  2.0539  1314   145  0.46  55.73   1.01     0.71      34806.18|
| 13:  2.0539 -  2.0000  1189   141  0.45  56.19   0.99     0.67      29820.14|
| 14:  2.0000 -  1.9513   367    35  0.38  61.49   0.93     0.56      27552.26|
|alpha:            min =        0.56 max =            0.90 mean =         0.78|
|beta:             min =    27552.26 max =        72260.16 mean =     46809.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.19|
|phase err.(test): min =        0.00 max =           89.85 mean =        44.25|
|-----------------------------------------------------------------------------|

============================== 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 = 6.955807              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.795   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.241247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.893   (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 |  1.530 -  1.867:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.867 -  2.204:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.204 -  2.541:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.541 -  2.878:     1254 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.878 -  3.215:     1926 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.215 -  3.552:     2535 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.552 -  3.889:     4709 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.889 -  4.226:     4590 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.226 -  4.563:     6147 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7334 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.530 |       0.404 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3804   r_free= 0.3840   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.170842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3655   r_free= 0.3710   ksol= 0.31   Bsol= 28.54   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-3.00,3.39,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.158988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.465164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.998   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.585007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.742   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3655      final r-factor (work) = 0.2501          |
| start r-factor (free) = 0.3710      final r-factor (free) = 0.2813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9962 = 5.47 * 0.50 * 6.1552 + 1.00 * 0.1767                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3703 = 5.47 * 0.50 * 5.9562 + 1.00 * 0.0944                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2501      final r-factor (work) = 0.2290          |
| start r-factor (free) = 0.2813      final r-factor (free) = 0.2884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4905 = 0.59 * 1.00 * 5.9562 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3877 = 0.59 * 1.00 * 5.7716 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.04   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    80.04   17.53    None  None   None       |
|    Sol.    : 438    0      3.09    80.04   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    79.05   13.46    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 -   8.004:  626   |   5:    40.021 -  48.026:  116        |
|      1:     8.004 -  16.009: 1170   |   6:    48.026 -  56.030:   78        |
|      2:    16.009 -  24.013:  439   |   7:    56.030 -  64.034:   48        |
|      3:    24.013 -  32.017:  178   |   8:    64.034 -  72.038:   26        |
|      4:    32.017 -  40.021:  134   |   9:    72.038 -  80.043:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2290 r_free = 0.2884             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2287 r_free = 0.2887             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2287   r_free= 0.2887   ksol= 0.31   Bsol= 28.54   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-3.00,3.39,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.780228                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2267   r_free= 0.2837   ksol= 0.30   Bsol= 28.54   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.48,0.13,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.770727                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.835179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.987   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261648              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.783  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2267      final r-factor (work) = 0.1627          |
| start r-factor (free) = 0.2837      final r-factor (free) = 0.2112          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1607 = 3.84 * 0.50 * 5.7709 + 1.00 * 0.0944                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8907 = 3.84 * 0.50 * 5.6475 + 1.00 * 0.0612                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1491          |
| start r-factor (free) = 0.2112      final r-factor (free) = 0.1965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4888 = 0.26 * 1.00 * 5.6475 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4759 = 0.26 * 1.00 * 5.4290 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.55   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    77.55   17.22    None  None   None       |
|    Sol.    : 438    0      6.49    76.82   39.63    None  None   None       |
|    Mac.    : 2385   0      0.00    77.55   13.11    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 -   7.755:  486   |   5:    38.776 -  46.531:  115        |
|      1:     7.755 -  15.510: 1371   |   6:    46.531 -  54.286:   98        |
|      2:    15.510 -  23.265:  405   |   7:    54.286 -  62.041:   43        |
|      3:    23.265 -  31.021:  137   |   8:    62.041 -  69.796:   26        |
|      4:    31.021 -  38.776:  130   |   9:    69.796 -  77.551:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1491 r_free = 0.1965             target_work(ml) = 5.392         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.1963             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.1963   ksol= 0.30   Bsol= 28.54   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.48,0.13,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.390907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.1954   ksol= 0.32   Bsol= 40.77   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.31,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.385530                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.635604              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.106  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.959849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.537   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1954      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2135 = 2.64 * 0.50 * 5.4275 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0564 = 2.64 * 0.50 * 5.3116 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.0412 = 3.96 * 1.00 * 5.3116 + 1.00 * 0.0081                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.6023 = 3.96 * 1.00 * 5.2002 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.53   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    95.53   17.70    None  None   None       |
|    Sol.    : 438    0      4.14    86.53   42.60    None  None   None       |
|    Mac.    : 2385   0      0.00    95.53   13.13    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 -   9.553:  925   |   5:    47.765 -  57.317:  107        |
|      1:     9.553 -  19.106: 1205   |   6:    57.317 -  66.870:   59        |
|      2:    19.106 -  28.659:  236   |   7:    66.870 -  76.423:   32        |
|      3:    28.659 -  38.212:  123   |   8:    76.423 -  85.976:   14        |
|      4:    38.212 -  47.765:  117   |   9:    85.976 -  95.529:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1632             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1631             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1631   ksol= 0.32   Bsol= 40.77   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.31,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1633   ksol= 0.32   Bsol= 45.05   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.37,-1.85,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188049                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.320928              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.445  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.744406              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4920 = 1.32 * 0.50 * 5.2012 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4702 = 1.32 * 0.50 * 5.1817 + 1.00 * 0.0479                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8675 = 0.74 * 1.00 * 5.1817 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8611 = 0.74 * 1.00 * 5.1737 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    99.42   17.44    None  None   None       |
|    all(noH): 2823   0      1.01    99.42   17.44    None  None   None       |
|    Sol.    : 438    0      4.87    88.99   41.62    None  None   None       |
|    Mac.    : 2385   0      1.01    99.42   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.009 -  10.850: 1238   |   5:    50.214 -  60.055:   97        |
|      1:    10.850 -  20.691:  969   |   6:    60.055 -  69.896:   35        |
|      2:    20.691 -  30.532:  198   |   7:    69.896 -  79.737:   31        |
|      3:    30.532 -  40.373:  131   |   8:    79.737 -  89.578:    6        |
|      4:    40.373 -  50.214:  114   |   9:    89.578 -  99.419:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1613             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1613             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1613   ksol= 0.32   Bsol= 45.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.37,-1.85,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1613   ksol= 0.32   Bsol= 45.04   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.18,-1.82,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.473788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.531  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4474 = 2.47 * 0.50 * 5.1738 + 1.00 * 0.0479                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4287 = 2.47 * 0.50 * 5.1456 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1038 = 0.80 * 1.00 * 5.1456 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0923 = 0.80 * 1.00 * 5.1314 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    103.98  17.17    None  None   None       |
|    all(noH): 2823   0      0.99    103.98  17.17    None  None   None       |
|    Sol.    : 438    0      6.11    90.81   40.78    None  None   None       |
|    Mac.    : 2385   0      0.99    103.98  12.83    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:     0.995 -  11.294: 1358   |   5:    52.490 -  62.789:   68        |
|      1:    11.294 -  21.593:  886   |   6:    62.789 -  73.087:   30        |
|      2:    21.593 -  31.892:  192   |   7:    73.087 -  83.386:   20        |
|      3:    31.892 -  42.191:  130   |   8:    83.386 -  93.685:    5        |
|      4:    42.191 -  52.490:  130   |   9:    93.685 - 103.984:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1077 r_free = 0.1576             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1576             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1576   ksol= 0.32   Bsol= 45.04   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.18,-1.82,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130346                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6589 0.99   1428  159 0.0940 0.1275      5.3494      5.5338|
|  2:  4.6589 -  3.7164 0.99   1387  150 0.0806 0.1046      5.3842      5.6008|
|  3:  3.7164 -  3.2521 0.99   1357  156 0.1015 0.1616      5.4326      5.8512|
|  4:  3.2521 -  2.9572 0.99   1343  148 0.1197 0.1525      5.4356      5.5832|
|  5:  2.9572 -  2.7467 0.99   1323  146 0.1249 0.1737      5.2859      5.4951|
|  6:  2.7467 -  2.5856 0.98   1326  152 0.1211 0.1811      5.1929      5.4224|
|  7:  2.5856 -  2.4567 0.99   1342  147 0.1199 0.1686      5.1411      5.3685|
|  8:  2.4567 -  2.3502 0.99   1312  145 0.1106 0.1717      5.0311      5.2743|
|  9:  2.3502 -  2.2600 0.98   1312  149 0.1130 0.1900      5.0008      5.3212|
| 10:  2.2600 -  2.1823 0.98   1313  148 0.1092 0.1647      4.9561      5.2051|
| 11:  2.1823 -  2.1142 0.98   1317  138 0.1112 0.1878      4.9259      5.2822|
| 12:  2.1142 -  2.0539 0.99   1314  145 0.1088 0.1681      4.8635      5.0737|
| 13:  2.0539 -  2.0000 0.90   1189  141 0.1096 0.1711      4.7558       5.004|
| 14:  2.0000 -  1.9513 0.27    367   35 0.1024 0.1674       4.602      4.9017|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6589  1428   159  0.94   8.48   0.98     0.95       6655.64|
|  2:  4.6589 -  3.7164  1387   150  0.95   7.75   1.02     1.01       8364.39|
|  3:  3.7164 -  3.2521  1357   156  0.94  10.86   1.03     1.03       9668.03|
|  4:  3.2521 -  2.9572  1343   148  0.92  14.02   1.01     0.99      10217.08|
|  5:  2.9572 -  2.7467  1323   146  0.90  15.87   0.99     0.97       7977.36|
|  6:  2.7467 -  2.5856  1326   152  0.90  16.13   0.99     0.96       6940.23|
|  7:  2.5856 -  2.4567  1342   147  0.91  15.02   0.99     0.97       6045.10|
|  8:  2.4567 -  2.3502  1312   145  0.91  15.41   0.99     0.95       5151.26|
|  9:  2.3502 -  2.2600  1312   149  0.90  15.79   1.00     0.97       4824.28|
| 10:  2.2600 -  2.1823  1313   148  0.91  15.34   0.99     0.96       4502.73|
| 11:  2.1823 -  2.1142  1317   138  0.90  16.60   0.99     0.96       4428.59|
| 12:  2.1142 -  2.0539  1314   145  0.90  16.34   1.00     0.99       4071.36|
| 13:  2.0539 -  2.0000  1189   141  0.91  15.50   0.99     0.98       3158.01|
| 14:  2.0000 -  1.9513   367    35  0.91  15.14   0.99     0.96       2311.27|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2311.27 max =        10217.08 mean =      6273.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.13 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1576   ksol= 0.32   Bsol= 45.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.97,-1.66,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1576   ksol= 0.32   Bsol= 45.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.97,-1.66,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130531                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6589 0.99   1428  159 0.0941 0.1276      5.3514      5.5353|
|  2:  4.6589 -  3.7164 0.99   1387  150 0.0805 0.1045      5.3843      5.6003|
|  3:  3.7164 -  3.2521 0.99   1357  156 0.1015 0.1616      5.4322      5.8511|
|  4:  3.2521 -  2.9572 0.99   1343  148 0.1197 0.1525      5.4355      5.5833|
|  5:  2.9572 -  2.7467 0.99   1323  146 0.1249 0.1738       5.286      5.4951|
|  6:  2.7467 -  2.5856 0.98   1326  152 0.1211 0.1813      5.1931      5.4228|
|  7:  2.5856 -  2.4567 0.99   1342  147 0.1199 0.1686      5.1414      5.3688|
|  8:  2.4567 -  2.3502 0.99   1312  145 0.1106 0.1717      5.0314      5.2746|
|  9:  2.3502 -  2.2600 0.98   1312  149 0.1130 0.1899       5.001      5.3209|
| 10:  2.2600 -  2.1823 0.98   1313  148 0.1092 0.1647       4.956      5.2048|
| 11:  2.1823 -  2.1142 0.98   1317  138 0.1112 0.1878      4.9259      5.2823|
| 12:  2.1142 -  2.0539 0.99   1314  145 0.1087 0.1680      4.8632      5.0733|
| 13:  2.0539 -  2.0000 0.90   1189  141 0.1096 0.1710      4.7557      5.0037|
| 14:  2.0000 -  1.9513 0.27    367   35 0.1024 0.1675      4.6021      4.9025|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6589  1428   159  0.94   8.50   0.98     0.95       6682.53|
|  2:  4.6589 -  3.7164  1387   150  0.95   7.76   1.02     1.01       8373.61|
|  3:  3.7164 -  3.2521  1357   156  0.94  10.86   1.04     1.04       9661.76|
|  4:  3.2521 -  2.9572  1343   148  0.92  14.02   1.01     0.99      10215.81|
|  5:  2.9572 -  2.7467  1323   146  0.90  15.87   1.00     0.97       7979.64|
|  6:  2.7467 -  2.5856  1326   152  0.90  16.14   0.99     0.96       6943.65|
|  7:  2.5856 -  2.4567  1342   147  0.91  15.03   1.00     0.97       6049.11|
|  8:  2.4567 -  2.3502  1312   145  0.91  15.41   0.99     0.96       5152.29|
|  9:  2.3502 -  2.2600  1312   149  0.90  15.79   1.01     0.97       4823.61|
| 10:  2.2600 -  2.1823  1313   148  0.91  15.34   1.00     0.97       4501.79|
| 11:  2.1823 -  2.1142  1317   138  0.90  16.60   1.00     0.96       4427.41|
| 12:  2.1142 -  2.0539  1314   145  0.90  16.34   1.01     1.00       4068.54|
| 13:  2.0539 -  2.0000  1189   141  0.91  15.50   1.00     0.99       3157.67|
| 14:  2.0000 -  1.9513   367    35  0.91  15.15   1.00     0.97       2312.71|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2312.71 max =        10215.81 mean =      6276.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.13 mean =        13.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.728)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    103.95  17.13    None  None   None       |
|    all(noH): 2823   0      0.96    103.95  17.13    None  None   None       |
|    Sol.    : 438    0      6.08    90.77   40.74    None  None   None       |
|    Mac.    : 2385   0      0.96    103.95  12.80    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:     0.960 -  11.259: 1358   |   5:    52.455 -  62.754:   68        |
|      1:    11.259 -  21.558:  886   |   6:    62.754 -  73.053:   30        |
|      2:    21.558 -  31.857:  192   |   7:    73.053 -  83.352:   20        |
|      3:    31.857 -  42.156:  130   |   8:    83.352 -  93.651:    5        |
|      4:    42.156 -  52.455:  130   |   9:    93.651 - 103.950:    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)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.617 - 5.843
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 317
   mapped sites are within: 0.773 - 5.843

peak=    5.902 closest distance to " NH2 ARG A  56 " =    2.177
peak=    5.403 closest distance to " CG  PRO A  54 " =    1.160
peak=    5.337 closest distance to " CB  SER A  63 " =    1.250
peak=    5.251 closest distance to " CB  GLN A 223 " =    1.491
peak=    5.171 closest distance to " O   HOH Z 126 " =    1.960
peak=    5.135 closest distance to " CB  GLN A 183 " =    1.259
peak=    5.018 closest distance to " NE2 GLN A  11 " =    1.115
peak=    5.016 closest distance to " O   HOH Z 232 " =    2.228
peak=    4.993 closest distance to " O   HOH Z 193 " =    1.815
peak=    4.764 closest distance to " O   HOH Z 144 " =    1.643
peak=    4.693 closest distance to " O   HOH Z  15 " =    2.136
peak=    4.625 closest distance to " CB  ASN A 148 " =    1.504
peak=    4.565 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.563 closest distance to " C   PRO A 198 " =    1.503
peak=    4.557 closest distance to " OD2 ASP A 286 " =    2.806
peak=    4.528 closest distance to " CB  PRO A  54 " =    0.858
peak=    4.524 closest distance to " O   HOH Z 368 " =    1.941
peak=    4.492 closest distance to " OD1 ASN A  69 " =    2.545
peak=    4.461 closest distance to " CB  GLU A 128 " =    1.125
peak=    4.459 closest distance to " CB  SER A   3 " =    1.404
peak=    4.445 closest distance to " O   HOH Z 260 " =    1.167
peak=    4.444 closest distance to " O   HOH Z 203 " =    1.838
peak=    4.438 closest distance to " CB  TYR A 169 " =    0.829
peak=    4.391 closest distance to " CB  LEU A 228 " =    1.113
peak=    4.379 closest distance to " CB  GLU A 152 " =    1.193
peak=    4.376 closest distance to " O   HOH Z 427 " =    2.855
peak=    4.335 closest distance to " O   HOH Z 236 " =    1.997
peak=    4.316 closest distance to " O   HOH Z  78 " =    1.819
peak=    4.311 closest distance to " O   HOH Z 278 " =    0.943
peak=    4.292 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.290 closest distance to " CA  ALA A  21 " =    1.141
peak=    4.278 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.269 closest distance to " O   HOH Z 108 " =    1.520
peak=    4.254 closest distance to " O   HOH Z 134 " =    1.444
peak=    4.189 closest distance to " CG  PRO A  90 " =    1.017
peak=    4.176 closest distance to " O   HOH Z 298 " =    1.875
peak=    4.166 closest distance to " O   HOH Z 316 " =    3.019
peak=    4.165 closest distance to " O   HOH Z 207 " =    1.859
peak=    4.163 closest distance to " CB  TRP A 179 " =    1.399
peak=    4.152 closest distance to " CB  VAL A 202 " =    1.719
peak=    4.139 closest distance to " O   HOH Z  61 " =    1.662
peak=    4.131 closest distance to " O   HOH Z 344 " =    3.014
peak=    4.120 closest distance to " CB  ASN A 148 " =    1.013
peak=    4.095 closest distance to " O   HOH Z 234 " =    3.690
peak=    4.087 closest distance to " O   HOH Z 371 " =    3.375
peak=    4.086 closest distance to " O   HOH Z 369 " =    1.967
peak=    4.083 closest distance to " O   HOH Z 180 " =    2.197
peak=    4.065 closest distance to " O   HOH Z 425 " =    1.364
peak=    4.064 closest distance to " CA  THR A 221 " =    0.974
peak=    4.028 closest distance to " ND2 ASN A 187 " =    1.613
peak=    4.007 closest distance to " O   HOH Z 389 " =    1.900
peak=    3.998 closest distance to " O   HOH Z 284 " =    3.009
peak=    3.987 closest distance to " CA  MET A  40 " =    1.061
peak=    3.979 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.963 closest distance to " CD BLYS A 290 " =    1.138
peak=    3.961 closest distance to " O   SER A  87 " =    2.260
peak=    3.961 closest distance to " O   HOH Z  93 " =    2.405
peak=    3.958 closest distance to " O   HOH Z 209 " =    2.323
peak=    3.955 closest distance to " CB  ARG A  79 " =    1.478
peak=    3.937 closest distance to " O   HOH Z  88 " =    3.425
peak=    3.927 closest distance to " O   HOH Z 193 " =    2.047
peak=    3.922 closest distance to " O   HOH Z  97 " =    1.867
peak=    3.915 closest distance to " CA  ASN A 215 " =    1.258
peak=    3.911 closest distance to " O   HOH Z 135 " =    1.737
peak=    3.890 closest distance to " O   HOH Z 346 " =    1.632
peak=    3.888 closest distance to " CB  VAL A 265 " =    1.195
peak=    3.874 closest distance to " O   HOH Z 261 " =    1.801
peak=    3.871 closest distance to " O   HOH Z 295 " =    1.519
peak=    3.866 closest distance to " CG2 THR A 221 " =    1.075
peak=    3.862 closest distance to " O   HOH Z   6 " =    2.181
peak=    3.844 closest distance to " O   HOH Z 108 " =    1.808
peak=    3.832 closest distance to " O   HOH Z 426 " =    1.470
peak=    3.824 closest distance to " O   HOH Z  48 " =    1.429
peak=    3.813 closest distance to " O   HOH Z 124 " =    1.380
peak=    3.811 closest distance to " O   HOH Z  10 " =    1.869
peak=    3.809 closest distance to " O   HOH Z  21 " =    1.679
peak=    3.807 closest distance to " NH2 ARG A 156 " =    1.226
peak=    3.798 closest distance to " O   MET A 105 " =    1.795
peak=    3.796 closest distance to " ND1 HIS A  86 " =    1.883
peak=    3.783 closest distance to " NH1AARG A 145 " =    1.025
peak=    3.781 closest distance to " O   HOH Z 128 " =    2.174
peak=    3.768 closest distance to " O   HOH Z 132 " =    2.353
peak=    3.764 closest distance to " O   HOH Z  68 " =    1.597
peak=    3.763 closest distance to " O   HOH Z 163 " =    1.926
peak=    3.758 closest distance to " CA  GLY A 241 " =    3.822
peak=    3.754 closest distance to " O   HOH Z 133 " =    1.620
peak=    3.748 closest distance to " CB  GLU A 277 " =    3.564
peak=    3.718 closest distance to " CD  LYS A 119 " =    1.182
peak=    3.717 closest distance to " O   HOH Z 156 " =    2.968
peak=    3.716 closest distance to " NH2BARG A 145 " =    2.023
peak=    3.711 closest distance to " O   HOH Z 411 " =    1.780
peak=    3.707 closest distance to " O   HOH Z 374 " =    2.591
peak=    3.701 closest distance to " O   HOH Z  59 " =    2.073
peak=    3.701 closest distance to " O   HOH Z 172 " =    3.779
peak=    3.701 closest distance to " O   HOH Z  54 " =    1.661
peak=    3.693 closest distance to " O   HOH Z 193 " =    1.582
peak=    3.690 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.688 closest distance to " O   HOH Z  20 " =    1.604
peak=    3.680 closest distance to " N   ARG A 156 " =    1.354
peak=    3.675 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.675 closest distance to " CA  THR A 264 " =    0.895
peak=    3.675 closest distance to " O   HOH Z 189 " =    1.967
peak=    3.670 closest distance to " O   ALA A 165 " =    1.375
peak=    3.661 closest distance to " O   HOH Z  43 " =    1.970
peak=    3.656 closest distance to " OG BSER A 164 " =    2.437
peak=    3.647 closest distance to " CB  MET A  47 " =    1.045
peak=    3.647 closest distance to " O   HOH Z 247 " =    1.245
peak=    3.644 closest distance to " O   HOH Z 303 " =    2.122
peak=    3.630 closest distance to " N   ASN A 127 " =    1.239
peak=    3.627 closest distance to " CB  SER A 141 " =    1.052
peak=    3.616 closest distance to " O   HOH Z 214 " =    1.915
peak=    3.614 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.607 closest distance to " CD1 LEU A 300 " =    1.225
peak=    3.603 closest distance to " NZ  LYS A 117 " =    3.281
peak=    3.602 closest distance to " CD2 LEU A 255 " =    1.403
peak=    3.600 closest distance to " O   HOH Z 250 " =    1.341
peak=    3.578 closest distance to " CA  ASN A 176 " =    1.225
peak=    3.570 closest distance to " O   HOH Z  54 " =    2.348
peak=    3.557 closest distance to " O   HOH Z 158 " =    2.896
peak=    3.551 closest distance to " O   HOH Z 272 " =    1.876
peak=    3.550 closest distance to " O   HOH Z 313 " =    1.632
peak=    3.547 closest distance to " CA  LYS A 117 " =    1.226
peak=    3.542 closest distance to " O   HOH Z 281 " =    4.343
peak=    3.542 closest distance to " CG  ARG A  66 " =    2.394
peak=    3.540 closest distance to " O   HOH Z  20 " =    2.273
peak=    3.535 closest distance to " O   HOH Z 409 " =    2.894
peak=    3.532 closest distance to " CB  ARG A 190 " =    1.720
peak=    3.528 closest distance to " CA  ALA A  51 " =    0.975
peak=    3.523 closest distance to " CB  ALA A 291 " =    1.467
peak=    3.522 closest distance to " O   HOH Z 334 " =    1.422
peak=    3.517 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.512 closest distance to " CD  ARG A 159 " =    0.813
peak=    3.512 closest distance to " CB  TYR A 169 " =    0.773
peak=    3.510 closest distance to " O   HOH Z 282 " =    1.429
peak=    3.503 closest distance to " O   HOH Z 403 " =    1.587
peak=    3.502 closest distance to " O   HOH Z  61 " =    1.657
peak=    3.500 closest distance to " O   HOH Z 279 " =    2.230
peak=    3.497 closest distance to " CD  LYS A 166 " =    1.311
peak=    3.492 closest distance to " O   HOH Z 263 " =    2.294
peak=    3.482 closest distance to " CB  GLU A 152 " =    1.508
peak=    3.481 closest distance to " ND1 HIS A  81 " =    1.472
peak=    3.480 closest distance to " CG  MET A 185 " =    1.115
peak=    3.479 closest distance to " O   HOH Z 173 " =    1.852
peak=    3.477 closest distance to " O   HOH Z 197 " =    2.788
peak=    3.468 closest distance to " O   HOH Z 128 " =    2.191
peak=    3.468 closest distance to " O   HOH Z  40 " =    1.595
peak=    3.467 closest distance to " O   HOH Z   1 " =    1.797
peak=    3.467 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.457 closest distance to " CG1BVAL A  72 " =    1.603
peak=    3.456 closest distance to " OG  SER A  22 " =    2.775
peak=    3.454 closest distance to " OE2 GLU A  53 " =    2.208
peak=    3.452 closest distance to " O   HOH Z 133 " =    2.307
peak=    3.445 closest distance to " O   HOH Z 407 " =    2.550
peak=    3.442 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.437 closest distance to " O   HOH Z 126 " =    1.576
peak=    3.430 closest distance to " O   ALA A 158 " =    1.260
peak=    3.427 closest distance to " O   HOH Z 403 " =    1.374
peak=    3.420 closest distance to " CE1 TYR A 186 " =    1.197
peak=    3.414 closest distance to " O   HOH Z 273 " =    2.806
peak=    3.411 closest distance to " O   HOH Z  63 " =    2.252
peak=    3.409 closest distance to " CA  ALA A 158 " =    1.118
peak=    3.404 closest distance to " O   HOH Z 326 " =    1.453
peak=    3.402 closest distance to " O   HOH Z 211 " =    2.201
peak=    3.401 closest distance to " O   HOH Z 388 " =    1.888
peak=    3.397 closest distance to " O   HOH Z  80 " =    1.633
peak=    3.391 closest distance to " O   HOH Z 425 " =    1.861
peak=    3.383 closest distance to " O   HOH Z  66 " =    2.057
peak=    3.377 closest distance to " NH1BARG A 145 " =    1.249
peak=    3.376 closest distance to " CB  ASP A 140 " =    0.899
peak=    3.376 closest distance to " O   HOH Z 118 " =    1.550
peak=    3.374 closest distance to " CB  SER A 216 " =    0.812
peak=    3.367 closest distance to " O   HOH Z 147 " =    1.662
peak=    3.366 closest distance to " OG  SER A  62 " =    3.065
peak=    3.364 closest distance to " CB  LEU A 143 " =    1.099
peak=    3.363 closest distance to " O   ALA A   1 " =    1.529
peak=    3.360 closest distance to " CG1 VAL A 202 " =    1.984
peak=    3.360 closest distance to " CG2 ILE A 120 " =    1.209
peak=    3.359 closest distance to " O   HOH Z 423 " =    1.891
peak=    3.358 closest distance to " O   HOH Z 271 " =    2.297
peak=    3.357 closest distance to " CA  ASP A 140 " =    1.131
peak=    3.354 closest distance to " O   HOH Z 276 " =    1.257
peak=    3.350 closest distance to " O   HOH Z  40 " =    1.857
peak=    3.349 closest distance to " O   HOH Z 286 " =    2.130
peak=    3.347 closest distance to " O   HOH Z 365 " =    2.783
peak=    3.344 closest distance to " O   HOH Z  44 " =    1.749
peak=    3.342 closest distance to " O   HOH Z 345 " =    3.342
peak=    3.341 closest distance to " O   HOH Z 291 " =    1.949
peak=    3.340 closest distance to " CD2 LEU A 297 " =    0.889
peak=    3.338 closest distance to " CD  ARG A 269 " =    0.890
peak=    3.337 closest distance to " O   HOH Z 353 " =    2.598
peak=    3.337 closest distance to " CB  ALA A 248 " =    0.922
peak=    3.333 closest distance to " O   HOH Z 368 " =    3.694
peak=    3.332 closest distance to " O   HOH Z 427 " =    3.105
peak=    3.331 closest distance to " O   HOH Z 337 " =    3.741
peak=    3.331 closest distance to " CG2 VAL A 257 " =    0.931
peak=    3.330 closest distance to " O   HOH Z 132 " =    0.904
peak=    3.329 closest distance to " CG AARG A 275 " =    1.007
peak=    3.329 closest distance to " CA  ALA A 291 " =    0.903
peak=    3.328 closest distance to " O   HOH Z 163 " =    1.827
peak=    3.327 closest distance to " CA  LEU A 282 " =    1.184
peak=    3.324 closest distance to " CA  ARG A 195 " =    1.355
peak=    3.320 closest distance to " OD1 ASP A 231 " =    1.859
peak=    3.318 closest distance to " O   HOH Z 189 " =    1.352
peak=    3.314 closest distance to " O   HOH Z 287 " =    2.193
peak=    3.310 closest distance to " O   GLY A  57 " =    2.485
peak=    3.309 closest distance to " C   LYS A 290 " =    1.364
peak=    3.306 closest distance to " CB  THR A 157 " =    0.997
peak=    3.304 closest distance to " O   HOH Z 116 " =    1.802
peak=    3.304 closest distance to " NH2 ARG A 219 " =    1.881
peak=    3.303 closest distance to " CD  PRO A 280 " =    1.011
peak=    3.302 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.301 closest distance to " O   HOH Z  68 " =    2.564
peak=    3.300 closest distance to " O   HOH Z 106 " =    2.333
peak=    3.299 closest distance to " CZ AARG A 102 " =    1.939
peak=    3.298 closest distance to " N   ASN A  39 " =    1.309
peak=    3.295 closest distance to " O   HOH Z   3 " =    1.623
peak=    3.292 closest distance to " NZ  LYS A  76 " =    1.218
peak=    3.286 closest distance to " CG1 ILE A 151 " =    0.850
peak=    3.286 closest distance to " O   HOH Z 327 " =    1.673
peak=    3.282 closest distance to " CD  PRO A 243 " =    1.612
peak=    3.281 closest distance to " O   HOH Z 248 " =    1.524
peak=    3.277 closest distance to " O   HOH Z 406 " =    1.622
peak=    3.275 closest distance to " CE2 TRP A 179 " =    1.611
peak=    3.274 closest distance to " O   HOH Z 345 " =    1.637
peak=    3.273 closest distance to " O   HOH Z 280 " =    1.662
peak=    3.271 closest distance to " O   HOH Z 183 " =    1.444
peak=    3.268 closest distance to " O   HOH Z  73 " =    1.453
peak=    3.265 closest distance to " CG  GLN A  88 " =    1.018
peak=    3.260 closest distance to " CA  VAL A 126 " =    1.204
peak=    3.256 closest distance to " O   HOH Z 236 " =    1.584
peak=    3.254 closest distance to " O   HOH Z  66 " =    2.071
peak=    3.250 closest distance to " O   HOH Z 128 " =    1.688
peak=    3.248 closest distance to " CB  SER A 212 " =    1.041
peak=    3.248 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.246 closest distance to " CA  ALA A 160 " =    0.822
peak=    3.243 closest distance to " NH2AARG A 190 " =    1.376
peak=    3.238 closest distance to " O   THR A 220 " =    1.437
peak=    3.235 closest distance to " O   HOH Z  44 " =    3.307
peak=    3.231 closest distance to " CB  GLU A  46 " =    1.045
peak=    3.230 closest distance to " O   HOH Z  49 " =    2.162
peak=    3.228 closest distance to " CG  MET A  93 " =    0.983
peak=    3.228 closest distance to " O   HOH Z 214 " =    2.468
peak=    3.228 closest distance to " CG2 VAL A 174 " =    1.314
peak=    3.222 closest distance to " O   HOH Z 174 " =    2.628
peak=    3.221 closest distance to " OG  SER A  97 " =    3.558
peak=    3.221 closest distance to " CD1 ILE A 106 " =    0.940
peak=    3.221 closest distance to " O   HOH Z 227 " =    2.190
peak=    3.218 closest distance to " C   ALA A   1 " =    1.646
peak=    3.217 closest distance to " CD1 ILE A  33 " =    1.573
peak=    3.216 closest distance to " OG ASER A  99 " =    2.032
peak=    3.212 closest distance to " CA  ALA A 233 " =    1.202
peak=    3.210 closest distance to " CA  TYR A 186 " =    1.427
peak=    3.210 closest distance to " O   HOH Z 106 " =    2.355
peak=    3.207 closest distance to " CA  GLY A 267 " =    1.182
peak=    3.204 closest distance to " CG  MET A 185 " =    1.186
peak=    3.204 closest distance to " O   HOH Z 359 " =    3.830
peak=    3.203 closest distance to " CA  ASP A 191 " =    0.812
peak=    3.203 closest distance to " O   HOH Z  64 " =    2.148
peak=    3.200 closest distance to " O   HOH Z 175 " =    3.582
peak=    3.198 closest distance to " O   HOH Z  63 " =    1.981
peak=    3.198 closest distance to " O   HOH Z 194 " =    2.087
peak=    3.196 closest distance to " CG  MET A 113 " =    1.367
peak=    3.196 closest distance to " O   HOH Z 115 " =    2.080
peak=    3.194 closest distance to " O   HOH Z  71 " =    1.060
peak=    3.192 closest distance to " O   HOH Z 261 " =    1.462
peak=    3.190 closest distance to " O   HOH Z 410 " =    1.909
peak=    3.187 closest distance to " CG  GLN A  77 " =    1.943
peak=    3.187 closest distance to " O   HOH Z 366 " =    3.099
peak=    3.186 closest distance to " CB  SER A  62 " =    1.266
peak=    3.182 closest distance to " O   HOH Z 166 " =    3.662
peak=    3.181 closest distance to " O   TRP A 274 " =    1.800
peak=    3.180 closest distance to " CA  TYR A 116 " =    1.476
peak=    3.178 closest distance to " O   HOH Z 211 " =    1.141
peak=    3.169 closest distance to " NE2 GLN A  58 " =    4.205
peak=    3.167 closest distance to " CD2 HIS A  81 " =    1.065
peak=    3.166 closest distance to " CB  SER A  26 " =    1.566
peak=    3.161 closest distance to " CB  TYR A 116 " =    0.924
peak=    3.159 closest distance to " CA  ALA A 154 " =    0.963
peak=    3.159 closest distance to " O   HOH Z 329 " =    3.385
peak=    3.155 closest distance to " O   HOH Z 368 " =    2.675
peak=    3.153 closest distance to " CG  GLN A  55 " =    2.118
peak=    3.152 closest distance to " O   HOH Z 125 " =    2.252
peak=    3.151 closest distance to " O   HOH Z 188 " =    1.990
peak=    3.151 closest distance to " O   HOH Z 234 " =    1.791
peak=    3.149 closest distance to " O   HOH Z  40 " =    2.521
peak=    3.142 closest distance to " CD  GLN A  58 " =    5.843
peak=    3.141 closest distance to " NZ  LYS A 166 " =    2.999
peak=    3.134 closest distance to " CB  PHE A 283 " =    0.810
peak=    3.133 closest distance to " OE1 GLU A 236 " =    1.319
peak=    3.129 closest distance to " CA  VAL A  41 " =    0.901
peak=    3.129 closest distance to " CA  ALA A 248 " =    1.176
peak=    3.121 closest distance to " CB  TYR A  30 " =    1.441
peak=    3.120 closest distance to " CG BARG A 275 " =    1.452
peak=    3.120 closest distance to " O   HOH Z 427 " =    3.647
peak=    3.118 closest distance to " NE AARG A 275 " =    1.466
peak=    3.114 closest distance to " CA  ARG A  36 " =    1.088
peak=    3.106 closest distance to " O   HOH Z 175 " =    2.175
peak=    3.104 closest distance to " O   HOH Z  53 " =    2.531
peak=    3.102 closest distance to " OE1 GLN A  11 " =    1.918
peak=    3.099 closest distance to " O   HOH Z 148 " =    3.654
peak=    3.093 closest distance to " O   HOH Z 357 " =    1.880
peak=    3.092 closest distance to " O   HOH Z 395 " =    1.429
peak=    3.081 closest distance to " CE BMET A  47 " =    1.257
peak=    3.080 closest distance to " O   HOH Z 423 " =    3.073
peak=    3.079 closest distance to " O   HOH Z  85 " =    2.101
peak=    3.065 closest distance to " C   GLY A  80 " =    1.143
peak=    3.063 closest distance to " CD1 LEU A 228 " =    2.012
peak=    3.060 closest distance to " CG  ARG A 269 " =    1.229
peak=    3.051 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.045 closest distance to " O   HOH Z 410 " =    1.712
peak=    3.029 closest distance to " CA  ILE A  33 " =    1.613
peak=    3.022 closest distance to " CB  PHE A  16 " =    0.975

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.638 - 5.402
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 208
   mapped sites are within: 0.845 - 5.402

peak=   -4.758 closest distance to " O   HOH Z 377 " =    1.870
peak=   -4.617 closest distance to " O   HOH Z 266 " =    4.249
peak=   -4.441 closest distance to " O   HOH Z 198 " =    2.286
peak=   -4.411 closest distance to " CD  ARG A 156 " =    1.927
peak=   -4.392 closest distance to " CB  PRO A 243 " =    2.583
peak=   -4.290 closest distance to " O   ILE A 109 " =    2.643
peak=   -4.209 closest distance to " OE1 GLN A 223 " =    2.118
peak=   -4.162 closest distance to " O   HOH Z 372 " =    2.435
peak=   -4.124 closest distance to " SG  CYS A 254 " =    3.300
peak=   -4.109 closest distance to " O   HOH Z  13 " =    1.406
peak=   -4.093 closest distance to " CE2 TYR A  30 " =    2.840
peak=   -4.089 closest distance to " N   MET A 188 " =    1.874
peak=   -4.085 closest distance to " O   HOH Z 290 " =    1.088
peak=   -4.055 closest distance to " O   HOH Z 231 " =    2.009
peak=   -3.982 closest distance to " O   HOH Z 102 " =    1.757
peak=   -3.965 closest distance to " O   HOH Z 388 " =    1.921
peak=   -3.940 closest distance to " N   ALA A  43 " =    2.469
peak=   -3.934 closest distance to " O   HOH Z  98 " =    1.835
peak=   -3.933 closest distance to " CD1 LEU A 228 " =    2.279
peak=   -3.929 closest distance to " OXT GLY A 302 " =    2.875
peak=   -3.910 closest distance to " O   PRO A 163 " =    2.027
peak=   -3.885 closest distance to " C   ASN A 285 " =    2.505
peak=   -3.882 closest distance to " O   HOH Z  11 " =    1.858
peak=   -3.878 closest distance to " O   HOH Z  93 " =    1.858
peak=   -3.870 closest distance to " O   PRO A 198 " =    1.324
peak=   -3.868 closest distance to " N   GLN A  58 " =    1.670
peak=   -3.840 closest distance to " O   HOH Z   3 " =    1.922
peak=   -3.829 closest distance to " CZ  PHE A  59 " =    1.632
peak=   -3.809 closest distance to " CG1 VAL A 250 " =    2.630
peak=   -3.787 closest distance to " CB  ASP A  27 " =    2.474
peak=   -3.784 closest distance to " O   HOH Z  43 " =    1.603
peak=   -3.781 closest distance to " O   SER A 210 " =    1.969
peak=   -3.766 closest distance to " O   HOH Z  52 " =    1.328
peak=   -3.755 closest distance to " CB  TYR A  15 " =    2.160
peak=   -3.742 closest distance to " O   VAL A  67 " =    2.840
peak=   -3.738 closest distance to " NH1 ARG A 195 " =    2.596
peak=   -3.731 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.721 closest distance to " ND2 ASN A  45 " =    1.117
peak=   -3.719 closest distance to " C   ALA A 158 " =    1.253
peak=   -3.718 closest distance to " O   HOH Z  10 " =    1.520
peak=   -3.710 closest distance to " CB  ASN A  39 " =    2.189
peak=   -3.707 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.706 closest distance to " O   HOH Z 185 " =    2.138
peak=   -3.698 closest distance to " CD  LYS A 289 " =    2.537
peak=   -3.694 closest distance to " CD  GLN A  88 " =    2.063
peak=   -3.683 closest distance to " O   HOH Z  11 " =    1.974
peak=   -3.681 closest distance to " C   HIS A 108 " =    1.078
peak=   -3.672 closest distance to " O   HOH Z 407 " =    3.187
peak=   -3.663 closest distance to " O   HOH Z 292 " =    4.506
peak=   -3.661 closest distance to " CD1 PHE A  59 " =    1.850
peak=   -3.628 closest distance to " O   HOH Z 353 " =    2.186
peak=   -3.624 closest distance to " CE  MET A  93 " =    1.207
peak=   -3.613 closest distance to " OG BSER A 134 " =    1.202
peak=   -3.605 closest distance to " O   HOH Z 385 " =    2.053
peak=   -3.604 closest distance to " OG ASER A 134 " =    1.262
peak=   -3.597 closest distance to " O   HOH Z  97 " =    1.792
peak=   -3.596 closest distance to " CG  PRO A 163 " =    2.446
peak=   -3.590 closest distance to " O   HOH Z 166 " =    1.425
peak=   -3.584 closest distance to " OD1 ASP A 191 " =    1.704
peak=   -3.584 closest distance to " O   SER A 135 " =    1.537
peak=   -3.578 closest distance to " N   THR A 157 " =    1.646
peak=   -3.575 closest distance to " CD1 LEU A 101 " =    2.454
peak=   -3.573 closest distance to " CB  ALA A 291 " =    2.387
peak=   -3.556 closest distance to " OG  SER A  62 " =    1.604
peak=   -3.555 closest distance to " CZ  TYR A 169 " =    1.753
peak=   -3.552 closest distance to " CB  ALA A  43 " =    2.295
peak=   -3.549 closest distance to " CA  SER A 146 " =    2.329
peak=   -3.547 closest distance to " O   ASP A 231 " =    2.570
peak=   -3.545 closest distance to " OG  SER A  97 " =    2.067
peak=   -3.542 closest distance to " O   HOH Z 395 " =    5.214
peak=   -3.536 closest distance to " O   HOH Z 118 " =    2.692
peak=   -3.532 closest distance to " CG  GLU A  53 " =    1.382
peak=   -3.530 closest distance to " O   HOH Z 435 " =    2.675
peak=   -3.525 closest distance to " O   VAL A 174 " =    2.092
peak=   -3.520 closest distance to " O   GLY A 211 " =    1.440
peak=   -3.516 closest distance to " CG  ASP A 231 " =    0.845
peak=   -3.506 closest distance to " CE  MET A 105 " =    2.091
peak=   -3.496 closest distance to " N   SER A 276 " =    1.273
peak=   -3.492 closest distance to " NH2 ARG A  79 " =    1.804
peak=   -3.487 closest distance to " CB  CYS A 254 " =    2.370
peak=   -3.479 closest distance to " O   HOH Z 166 " =    1.795
peak=   -3.471 closest distance to " CB  SER A 245 " =    2.472
peak=   -3.464 closest distance to " O   VAL A  67 " =    2.755
peak=   -3.463 closest distance to " NH2 ARG A  66 " =    2.101
peak=   -3.460 closest distance to " CE2 PHE A 218 " =    2.476
peak=   -3.455 closest distance to " O   HOH Z  38 " =    1.550
peak=   -3.442 closest distance to " N   ALA A 248 " =    1.581
peak=   -3.441 closest distance to " CB  ALA A 291 " =    2.226
peak=   -3.435 closest distance to " C   LEU A 143 " =    1.335
peak=   -3.432 closest distance to " O   HOH Z 148 " =    3.259
peak=   -3.431 closest distance to " CE3 TRP A 274 " =    2.458
peak=   -3.429 closest distance to " NH2AARG A 275 " =    5.402
peak=   -3.427 closest distance to " OH  TYR A 214 " =    1.281
peak=   -3.423 closest distance to " CB  CYS A 201 " =    2.492
peak=   -3.422 closest distance to " O   HOH Z 266 " =    4.490
peak=   -3.419 closest distance to " CZ3 TRP A 179 " =    1.278
peak=   -3.415 closest distance to " O   HOH Z 283 " =    1.711
peak=   -3.415 closest distance to " OG  SER A  87 " =    1.291
peak=   -3.411 closest distance to " OG BSER A 134 " =    1.681
peak=   -3.400 closest distance to " SG ACYS A 201 " =    1.987
peak=   -3.399 closest distance to " CG  LEU A  83 " =    1.941
peak=   -3.399 closest distance to " CG  PHE A 283 " =    2.742
peak=   -3.394 closest distance to " OD2 ASP A 171 " =    2.187
peak=   -3.386 closest distance to " O   HOH Z 396 " =    1.622
peak=   -3.385 closest distance to " O   HOH Z 275 " =    1.536
peak=   -3.381 closest distance to " O   HOH Z 234 " =    4.105
peak=   -3.380 closest distance to " O   HOH Z  71 " =    1.239
peak=   -3.379 closest distance to " OD1 ASN A 148 " =    1.666
peak=   -3.379 closest distance to " O   HOH Z 436 " =    1.384
peak=   -3.375 closest distance to " CG1 VAL A 112 " =    2.774
peak=   -3.372 closest distance to " CB  ALA A 131 " =    2.038
peak=   -3.372 closest distance to " OD1 ASP A 171 " =    1.508
peak=   -3.371 closest distance to " O   HOH Z 361 " =    3.434
peak=   -3.369 closest distance to " O   VAL A 153 " =    2.351
peak=   -3.368 closest distance to " CG1 VAL A 197 " =    2.315
peak=   -3.366 closest distance to " O   GLY A 196 " =    1.102
peak=   -3.364 closest distance to " OE1 GLN A  77 " =    1.753
peak=   -3.353 closest distance to " N   HIS A 115 " =    1.702
peak=   -3.353 closest distance to " O   PHE A 218 " =    1.516
peak=   -3.351 closest distance to " CB  PRO A 163 " =    2.587
peak=   -3.350 closest distance to " CA  GLY A 133 " =    1.939
peak=   -3.343 closest distance to " O   HOH Z 409 " =    4.536
peak=   -3.341 closest distance to " OD1 ASN A 187 " =    1.633
peak=   -3.338 closest distance to " NH1 ARG A  56 " =    2.535
peak=   -3.336 closest distance to " O   ALA A 161 " =    1.590
peak=   -3.333 closest distance to " O   HOH Z  98 " =    1.416
peak=   -3.329 closest distance to " O   HOH Z  76 " =    1.951
peak=   -3.328 closest distance to " N   ALA A 226 " =    2.086
peak=   -3.327 closest distance to " O   HOH Z 348 " =    1.821
peak=   -3.322 closest distance to " O   HOH Z 278 " =    2.402
peak=   -3.320 closest distance to " CD2 LEU A 237 " =    2.325
peak=   -3.295 closest distance to " O   HOH Z  63 " =    1.325
peak=   -3.289 closest distance to " CB  ALA A 248 " =    1.927
peak=   -3.289 closest distance to " O   HOH Z 389 " =    1.787
peak=   -3.287 closest distance to " CB  ALA A  51 " =    1.852
peak=   -3.284 closest distance to " O   HOH Z  60 " =    2.372
peak=   -3.281 closest distance to " OG1 THR A 178 " =    1.193
peak=   -3.280 closest distance to " O   HOH Z 148 " =    1.801
peak=   -3.279 closest distance to " CG  GLN A 278 " =    2.273
peak=   -3.279 closest distance to " CE  LYS A  76 " =    2.654
peak=   -3.271 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.266 closest distance to " O   MET A  40 " =    2.822
peak=   -3.262 closest distance to " O   HOH Z 310 " =    3.469
peak=   -3.260 closest distance to " O   HOH Z 311 " =    3.610
peak=   -3.259 closest distance to " NH2 ARG A 159 " =    2.489
peak=   -3.254 closest distance to " O   HOH Z  88 " =    2.093
peak=   -3.252 closest distance to " CB  PHE A 192 " =    1.859
peak=   -3.250 closest distance to " O   HOH Z 198 " =    1.521
peak=   -3.250 closest distance to " CB  ASP A 132 " =    2.303
peak=   -3.248 closest distance to " O   HOH Z   9 " =    2.112
peak=   -3.246 closest distance to " O   HOH Z 394 " =    1.499
peak=   -3.244 closest distance to " O   HOH Z 350 " =    1.615
peak=   -3.236 closest distance to " NH1BARG A 275 " =    2.128
peak=   -3.234 closest distance to " O   PRO A 198 " =    1.321
peak=   -3.227 closest distance to " O   ASN A 249 " =    1.604
peak=   -3.226 closest distance to " O   HOH Z   6 " =    1.634
peak=   -3.223 closest distance to " O   HOH Z 252 " =    4.365
peak=   -3.220 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.219 closest distance to " O   HOH Z  15 " =    1.638
peak=   -3.218 closest distance to " CG2 VAL A 189 " =    2.055
peak=   -3.212 closest distance to " O   HOH Z  47 " =    1.452
peak=   -3.212 closest distance to " O   HOH Z 263 " =    2.996
peak=   -3.211 closest distance to " O   HOH Z 298 " =    1.239
peak=   -3.209 closest distance to " O   GLY A 118 " =    2.188
peak=   -3.207 closest distance to " O   HOH Z  90 " =    3.070
peak=   -3.197 closest distance to " O   HOH Z 137 " =    1.495
peak=   -3.195 closest distance to " O   HOH Z 359 " =    3.000
peak=   -3.192 closest distance to " O   HOH Z 309 " =    2.399
peak=   -3.184 closest distance to " CG  GLN A  88 " =    0.873
peak=   -3.180 closest distance to " C   GLN A 240 " =    2.290
peak=   -3.180 closest distance to " O   HOH Z 265 " =    1.874
peak=   -3.179 closest distance to " CG  GLU A 152 " =    2.206
peak=   -3.178 closest distance to " OD2 ASP A 171 " =    1.710
peak=   -3.173 closest distance to " NH2 ARG A  66 " =    4.859
peak=   -3.170 closest distance to " OG  SER A 245 " =    1.065
peak=   -3.167 closest distance to " O   ILE A 263 " =    1.901
peak=   -3.162 closest distance to " O   HOH Z 417 " =    2.476
peak=   -3.161 closest distance to " CE3 TRP A  70 " =    1.855
peak=   -3.161 closest distance to " CB  LEU A 167 " =    2.133
peak=   -3.161 closest distance to " ND2 ASN A 249 " =    2.159
peak=   -3.161 closest distance to " O   HOH Z 143 " =    2.501
peak=   -3.152 closest distance to " N   THR A 264 " =    1.361
peak=   -3.148 closest distance to " CG2 ILE A  49 " =    2.697
peak=   -3.145 closest distance to " CG  TRP A 266 " =    1.578
peak=   -3.141 closest distance to " CA  TRP A 274 " =    1.599
peak=   -3.138 closest distance to " CG2 ILE A 263 " =    2.262
peak=   -3.133 closest distance to " O   ALA A  51 " =    1.368
peak=   -3.132 closest distance to " O   VAL A 125 " =    2.262
peak=   -3.130 closest distance to " O   HOH Z 313 " =    2.061
peak=   -3.128 closest distance to " CG  ARG A 269 " =    2.402
peak=   -3.125 closest distance to " CB  ASP A 132 " =    2.271
peak=   -3.125 closest distance to " OD1 ASP A 200 " =    1.336
peak=   -3.124 closest distance to " O   VAL A 197 " =    1.194
peak=   -3.121 closest distance to " OE1 GLN A  88 " =    1.259
peak=   -3.110 closest distance to " CZ  PHE A  38 " =    2.448
peak=   -3.110 closest distance to " CZ  ARG A 259 " =    0.912
peak=   -3.096 closest distance to " CG2 ILE A  20 " =    2.760
peak=   -3.093 closest distance to " O   HOH Z 222 " =    1.273
peak=   -3.090 closest distance to " O   HOH Z 108 " =    2.408
peak=   -3.088 closest distance to " OG ASER A 216 " =    1.012
peak=   -3.077 closest distance to " O   HOH Z 139 " =    2.887
peak=   -3.057 closest distance to " CB  ASP A 132 " =    2.232
peak=   -3.044 closest distance to " O   PRO A 198 " =    1.726
peak=   -3.035 closest distance to " O   HOH Z 119 " =    4.194
peak=   -3.028 closest distance to " CB  PHE A  16 " =    2.565
peak=   -3.025 closest distance to " CG  GLN A  58 " =    1.202

================= 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    :  0.3804 0.3840   6.170842e+00   6.181988e+00
   1_bss:  0.3655 0.3710   6.158988e+00   6.159106e+00
   1_xyz:  0.2501 0.2813   5.826801e+00   5.930540e+00
   1_adp:  0.2290 0.2884   5.781178e+00   5.950635e+00
   1_occ:  0.2287 0.2887   5.780228e+00   5.950014e+00
   2_bss:  0.2267 0.2837   5.770727e+00   5.938361e+00
   2_xyz:  0.1627 0.2112   5.467208e+00   5.666533e+00
   2_adp:  0.1491 0.1965   5.392170e+00   5.599107e+00
   2_occ:  0.1490 0.1963   5.390907e+00   5.598317e+00
   3_bss:  0.1482 0.1954   5.385530e+00   5.593474e+00
   3_xyz:  0.1242 0.1656   5.223113e+00   5.444118e+00
   3_adp:  0.1183 0.1632   5.188308e+00   5.420415e+00
   3_occ:  0.1183 0.1631   5.187842e+00   5.420101e+00
   4_bss:  0.1185 0.1633   5.188049e+00   5.420610e+00
   4_xyz:  0.1159 0.1615   5.176372e+00   5.408258e+00
   4_adp:  0.1151 0.1613   5.171904e+00   5.404421e+00
   4_occ:  0.1150 0.1613   5.171654e+00   5.404456e+00
   5_bss:  0.1150 0.1613   5.171687e+00   5.404459e+00
   5_xyz:  0.1083 0.1583   5.133780e+00   5.384799e+00
   5_adp:  0.1077 0.1576   5.130339e+00   5.382296e+00
   5_occ:  0.1076 0.1576   5.130346e+00   5.382601e+00
   5_bss:  0.1076 0.1576   5.130531e+00   5.382687e+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:  0.311  28.536  -1.659  -3.005   3.386  -0.000   0.000   0.000
   1_xyz:  0.311  28.536  -1.659  -3.005   3.386  -0.000   0.000   0.000
   1_adp:  0.311  28.536  -1.659  -3.005   3.386  -0.000   0.000   0.000
   1_occ:  0.311  28.536  -1.659  -3.005   3.386  -0.000   0.000   0.000
   2_bss:  0.301  28.536  -1.992  -2.477   0.129  -0.000   0.000   0.000
   2_xyz:  0.301  28.536  -1.992  -2.477   0.129  -0.000   0.000   0.000
   2_adp:  0.301  28.536  -1.992  -2.477   0.129  -0.000   0.000   0.000
   2_occ:  0.301  28.536  -1.992  -2.477   0.129  -0.000   0.000   0.000
   3_bss:  0.318  40.766  -2.154  -2.282  -1.306  -0.000  -0.000  -0.000
   3_xyz:  0.318  40.766  -2.154  -2.282  -1.306  -0.000  -0.000  -0.000
   3_adp:  0.318  40.766  -2.154  -2.282  -1.306  -0.000  -0.000  -0.000
   3_occ:  0.318  40.766  -2.154  -2.282  -1.306  -0.000  -0.000  -0.000
   4_bss:  0.317  45.049  -2.293  -2.367  -1.852  -0.000  -0.000  -0.000
   4_xyz:  0.317  45.049  -2.293  -2.367  -1.852  -0.000  -0.000  -0.000
   4_adp:  0.317  45.049  -2.293  -2.367  -1.852  -0.000  -0.000  -0.000
   4_occ:  0.317  45.049  -2.293  -2.367  -1.852  -0.000  -0.000  -0.000
   5_bss:  0.318  45.045  -2.134  -2.176  -1.823  -0.000  -0.000  -0.000
   5_xyz:  0.318  45.045  -2.134  -2.176  -1.823  -0.000  -0.000  -0.000
   5_adp:  0.318  45.045  -2.134  -2.176  -1.823  -0.000  -0.000  -0.000
   5_occ:  0.318  45.045  -2.134  -2.176  -1.823  -0.000  -0.000  -0.000
   5_bss:  0.320  44.997  -1.937  -1.974  -1.660  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.195 0.5934  0.7808    46812.222
   1_bss:  42.600 0.6105  0.7935    42632.157
   1_xyz:  29.279 0.7665  0.9522    22094.298
   1_adp:  30.436 0.7527  0.9404    23235.490
   1_occ:  30.438 0.7526  0.9401    23203.440
   2_bss:  29.751 0.7601  0.9150    22407.559
   2_xyz:  20.814 0.8530  0.9852    11540.787
   2_adp:  18.822 0.8729  0.9938     9995.406
   2_occ:  18.789 0.8732  0.9937     9966.515
   3_bss:  18.638 0.8747  0.9783     9904.893
   3_xyz:  15.325 0.9036  0.9916     7101.168
   3_adp:  14.778 0.9084  0.9883     6785.345
   3_occ:  14.765 0.9086  0.9883     6782.671
   4_bss:  14.767 0.9086  0.9792     6811.031
   4_xyz:  14.503 0.9109  0.9791     6604.484
   4_adp:  14.402 0.9119  0.9750     6575.113
   4_occ:  14.394 0.9120  0.9748     6572.259
   5_bss:  14.396 0.9120  0.9791     6574.253
   5_xyz:  14.063 0.9145  0.9804     6317.116
   5_adp:  13.991 0.9151  0.9755     6273.067
   5_occ:  13.990 0.9151  0.9754     6274.065
   5_bss:  13.994 0.9151  0.9807     6276.785
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7666e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7666e-01
   1_xyz:   1.281  0.010  0.079 15.673  0.005  4.111   9.4432e-02
   1_adp:   1.281  0.010  0.079 15.673  0.005  4.111   9.4432e-02
   1_occ:   1.281  0.010  0.079 15.673  0.005  4.111   9.4432e-02
   2_bss:   1.281  0.010  0.079 15.673  0.005  4.111   9.4432e-02
   2_xyz:   1.043  0.007  0.071 14.357  0.004  4.123   6.1153e-02
   2_adp:   1.043  0.007  0.071 14.357  0.004  4.123   6.1153e-02
   2_occ:   1.043  0.007  0.071 14.357  0.004  4.123   6.1153e-02
   3_bss:   1.043  0.007  0.071 14.357  0.004  4.123   6.1153e-02
   3_xyz:   0.976  0.006  0.070 14.679  0.004  4.110   5.6778e-02
   3_adp:   0.976  0.006  0.070 14.679  0.004  4.110   5.6778e-02
   3_occ:   0.976  0.006  0.070 14.679  0.004  4.110   5.6778e-02
   4_bss:   0.976  0.006  0.070 14.679  0.004  4.110   5.6778e-02
   4_xyz:   0.882  0.005  0.065 14.410  0.003  4.111   4.7923e-02
   4_adp:   0.882  0.005  0.065 14.410  0.003  4.111   4.7923e-02
   4_occ:   0.882  0.005  0.065 14.410  0.003  4.111   4.7923e-02
   5_bss:   0.882  0.005  0.065 14.410  0.003  4.111   4.7923e-02
   5_xyz:   1.058  0.007  0.076 14.854  0.004  4.112   6.4081e-02
   5_adp:   1.058  0.007  0.076 14.854  0.004  4.112   6.4081e-02
   5_occ:   1.058  0.007  0.076 14.854  0.004  4.112   6.4081e-02
   5_bss:   1.058  0.007  0.076 14.854  0.004  4.112   6.4081e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.530   2.4001e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.530   2.4001e-01
   1_xyz:   8.900  0.050  0.277 88.377  0.033  2.227   1.1442e-01
   1_adp:   8.900  0.050  0.277 88.377  0.033  2.227   1.1442e-01
   1_occ:   8.900  0.050  0.277 88.377  0.033  2.227   1.1442e-01
   2_bss:   8.900  0.050  0.277 88.377  0.033  2.227   1.1442e-01
   2_xyz:   6.768  0.050  0.256 79.995  0.028  2.395   6.4413e-02
   2_adp:   6.768  0.050  0.256 79.995  0.028  2.395   6.4413e-02
   2_occ:   6.768  0.050  0.256 79.995  0.028  2.395   6.4413e-02
   3_bss:   6.768  0.050  0.256 79.995  0.028  2.395   6.4413e-02
   3_xyz:   7.270  0.042  0.261 84.159  0.031  2.308   4.4795e-02
   3_adp:   7.270  0.042  0.261 84.159  0.031  2.308   4.4795e-02
   3_occ:   7.270  0.042  0.261 84.159  0.031  2.308   4.4795e-02
   4_bss:   7.270  0.042  0.261 84.159  0.031  2.308   4.4795e-02
   4_xyz:   7.006  0.044  0.203 83.244  0.027  2.402   2.8661e-02
   4_adp:   7.006  0.044  0.203 83.244  0.027  2.402   2.8661e-02
   4_occ:   7.006  0.044  0.203 83.244  0.027  2.402   2.8661e-02
   5_bss:   7.006  0.044  0.203 83.244  0.027  2.402   2.8661e-02
   5_xyz:   7.054  0.040  0.245 83.454  0.033  2.268   4.6921e-02
   5_adp:   7.054  0.040  0.245 83.454  0.033  2.268   4.6921e-02
   5_occ:   7.054  0.040  0.245 83.454  0.033  2.268   4.6921e-02
   5_bss:   7.054  0.040  0.245 83.454  0.033  2.268   4.6921e-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:  80.04   0.00  17.53  79.05   0.00  13.46  80.04   3.09  39.73
   1_occ:  80.04   0.00  17.53  79.05   0.00  13.46  80.04   3.09  39.73
   2_bss:  80.04   0.00  17.53  79.05   0.00  13.46  80.04   3.09  39.73
   2_xyz:  80.04   0.00  17.53  79.05   0.00  13.46  80.04   3.09  39.73
   2_adp:  77.55   0.00  17.22  77.55   0.00  13.11  76.82   6.49  39.63
   2_occ:  77.55   0.00  17.22  77.55   0.00  13.11  76.82   6.49  39.63
   3_bss:  77.55   0.00  17.22  77.55   0.00  13.11  76.82   6.49  39.63
   3_xyz:  77.55   0.00  17.22  77.55   0.00  13.11  76.82   6.49  39.63
   3_adp:  95.53   0.00  17.70  95.53   0.00  13.13  86.53   4.14  42.60
   3_occ:  95.53   0.00  17.70  95.53   0.00  13.13  86.53   4.14  42.60
   4_bss:  95.53   0.00  17.70  95.53   0.00  13.13  86.53   4.14  42.60
   4_xyz:  95.53   0.00  17.70  95.53   0.00  13.13  86.53   4.14  42.60
   4_adp:  99.42   1.01  17.44  99.42   1.01  13.00  88.99   4.87  41.62
   4_occ:  99.42   1.01  17.44  99.42   1.01  13.00  88.99   4.87  41.62
   5_bss:  99.42   1.01  17.44  99.42   1.01  13.00  88.99   4.87  41.62
   5_xyz:  99.42   1.01  17.44  99.42   1.01  13.00  88.99   4.87  41.62
   5_adp: 103.98   0.99  17.17 103.98   0.99  12.83  90.81   6.11  40.78
   5_occ: 103.98   0.99  17.17 103.98   0.99  12.83  90.81   6.11  40.78
   5_bss: 103.95   0.96  17.13 103.95   0.96  12.80  90.77   6.08  40.74
------------------------------------------------------------------------
 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:    1.880    0.006    0.344
   1_adp:    1.880    0.006    0.344
   1_occ:    1.880    0.006    0.344
   2_bss:    1.880    0.006    0.344
   2_xyz:    1.384    0.029    0.449
   2_adp:    1.384    0.029    0.449
   2_occ:    1.384    0.029    0.449
   3_bss:    1.384    0.029    0.449
   3_xyz:    1.422    0.027    0.504
   3_adp:    1.422    0.027    0.504
   3_occ:    1.422    0.027    0.504
   4_bss:    1.422    0.027    0.504
   4_xyz:    1.453    0.040    0.513
   4_adp:    1.453    0.040    0.513
   4_occ:    1.453    0.040    0.513
   5_bss:    1.453    0.040    0.513
   5_xyz:    1.555    0.035    0.530
   5_adp:    1.555    0.035    0.530
   5_occ:    1.555    0.035    0.530
   5_bss:    1.555    0.035    0.530
------------------------------------------------------------------------

CPU time actual refinement: 368.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/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_902/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_902/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.94 
  Macro-tasks:
    bulk solvent and scale       = 36.33  
    individual site refinement   = 162.08 
    weights calculation          = 29.91  
    collect and process          = 6.53   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 234.93 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 124.71 
    alpha_beta                      = 7.85   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 134.15 
    fmodel                         = 6.76   
    r_factors                      = 0.15   
    phase_errors                   = 11.03  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 287.92 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.094 micro seconds
Total CPU time: 6.36 minutes
from_scatterers_fft:    676 calls, 124.35 s
gradients_fft:          621 calls, 119.60 s

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

# Date 2008-01-16 Time 05:57:29 PST -0800 (1200491849.15 s)
Start R-work = 0.3804, R-free = 0.3840 (no bulk solvent and anisotropic scale)
Final R-work = 0.1315, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.3655, R-free = 0.3710
Final R-work = 0.1076, R-free = 0.1576