# Date 2008-01-16 Time 06:53:14 PST -0800 (1200495194.46 s)
#phil __OFF__

Command line arguments: "../1322.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16700
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1322

-------------------------------------------------------------------------------
  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: (72.0062, 48.1033, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97153
Completeness in resolution range: 0.913666
Completeness with d_max=infinity: 0.910989

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9715

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: (72.0062, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97153
Completeness in resolution range: 0.913666
Completeness with d_max=infinity: 0.910989

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2201 [2255/2284]  2031   224   9.9%
  bin  2:  4.2201 -  3.3615 [2150/2173]  1933   217  10.1%
  bin  3:  3.3615 -  2.9401 [2128/2153]  1915   213  10.0%
  bin  4:  2.9401 -  2.6729 [2118/2134]  1908   210   9.9%
  bin  5:  2.6729 -  2.4822 [2081/2125]  1877   204   9.8%
  bin  6:  2.4822 -  2.3364 [2096/2124]  1883   213  10.2%
  bin  7:  2.3364 -  2.2197 [2095/2131]  1886   209  10.0%
  bin  8:  2.2197 -  2.1234 [2050/2092]  1845   205  10.0%
  bin  9:  2.1234 -  2.0418 [2020/2118]  1815   205  10.1%
  bin 10:  2.0418 -  1.9715 [ 596/2106]   537    59   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/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:
        1.24 -     1.98: 8
        1.98 -     2.71: 160
        2.71 -     3.44: 4480
        3.44 -     4.17: 9285
        4.17 -     4.90: 14050
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.245 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.333 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.444 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.550 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.747 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27978 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_1322/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/model_refine_001.geo

CPU time processing inputs: 8.12


============================ 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 = 72.00625 48.10325 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4884   r_free= 0.4711   ksol= 0.00   Bsol= 0.00   scale= 0.863    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.296714                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7076 0.99   1463  166 0.3895 0.4157      6.5915       6.599|
|  2:  4.7076 -  3.7551 0.99   1397  154 0.4344 0.4269      6.8826      6.8741|
|  3:  3.7551 -  3.2859 0.99   1383  148 0.4761 0.4323       6.694      6.6494|
|  4:  3.2859 -  2.9879 0.99   1364  154 0.4936 0.4712       6.526      6.5151|
|  5:  2.9879 -  2.7752 0.99   1367  152 0.5078 0.5142      6.3631      6.3748|
|  6:  2.7752 -  2.6124 0.99   1355  154 0.5306 0.4986      6.2858      6.1898|
|  7:  2.6124 -  2.4822 0.98   1335  140 0.5228 0.4510      6.2456      6.2017|
|  8:  2.4822 -  2.3745 0.98   1343  152 0.5235 0.5013      6.1495      6.1807|
|  9:  2.3745 -  2.2834 0.99   1350  154 0.5488 0.5141      6.1516      6.0965|
| 10:  2.2834 -  2.2049 0.98   1334  149 0.5203 0.5031      6.0631      6.1241|
| 11:  2.2049 -  2.1361 0.97   1334  143 0.5403 0.5272      6.0414      5.9772|
| 12:  2.1361 -  2.0752 0.99   1307  149 0.5096 0.5217      5.9199      5.9766|
| 13:  2.0752 -  2.0207 0.76   1037  121 0.5220 0.4320      5.8636      5.8134|
| 14:  2.0207 -  1.9715 0.19    261   23 0.5718 0.4909      5.7904      5.7626|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7076  1463   166  0.67  36.62   0.81     0.72      80776.39|
|  2:  4.7076 -  3.7551  1397   154  0.67  37.51   0.88     0.76     114093.51|
|  3:  3.7551 -  3.2859  1383   148  0.54  48.38   0.87     0.71     125237.49|
|  4:  3.2859 -  2.9879  1364   154  0.45  56.18   0.86     0.62     112741.67|
|  5:  2.9879 -  2.7752  1367   152  0.36  62.66   0.84     0.53      90904.96|
|  6:  2.7752 -  2.6124  1355   154  0.36  63.01   0.86     0.51      74219.01|
|  7:  2.6124 -  2.4822  1335   140  0.36  62.77   0.89     0.50      64132.14|
|  8:  2.4822 -  2.3745  1343   152  0.36  63.27   0.86     0.53      59505.76|
|  9:  2.3745 -  2.2834  1350   154  0.35  63.98   0.90     0.51      53244.61|
| 10:  2.2834 -  2.2049  1334   149  0.34  64.37   0.90     0.51      51117.41|
| 11:  2.2049 -  2.1361  1334   143  0.30  67.52   0.90     0.45      48061.70|
| 12:  2.1361 -  2.0752  1307   149  0.29  68.81   0.90     0.46      45215.78|
| 13:  2.0752 -  2.0207  1037   121  0.31  66.60   0.92     0.49      36546.05|
| 14:  2.0207 -  1.9715   261    23  0.37  61.88   0.86     0.60      26727.71|
|alpha:            min =        0.45 max =            0.76 mean =         0.57|
|beta:             min =    26727.71 max =       125237.49 mean =     73912.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.24|
|phase err.(test): min =        0.00 max =           89.92 mean =        58.12|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.251760             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.763   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.352296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.558   (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 |  1.245 -  1.610:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.610 -  1.976:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.976 -  2.341:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.341 -  2.707:      142 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.707 -  3.072:     2233 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.072 -  3.438:     2247 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.438 -  3.803:     4047 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.803 -  4.169:     5238 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.169 -  4.534:     6298 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.534 -  4.900:     7752 |
|-----------------------------------------------------------------------------|
|-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 |        0.189 |
| 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  1.245 |       0.542 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4884   r_free= 0.4711   ksol= 0.00   Bsol= 0.00   scale= 0.863    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.296714                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4823   r_free= 0.4630   ksol= 0.26   Bsol= 11.63   scale= 0.908   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,3.19,-0.73,0.00,-0.00,-0.00); trace/3= 1.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.293894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.822172             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.611   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.583278              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.349   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4823      final r-factor (work) = 0.3887          |
| start r-factor (free) = 0.4630      final r-factor (free) = 0.4299          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.8083 = 14.82 * 0.50 * 6.2905 + 1.00 * 0.1890                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0489 = 14.82 * 0.50 * 6.1918 + 1.00 * 0.1609                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3887      final r-factor (work) = 0.3567          |
| start r-factor (free) = 0.4299      final r-factor (free) = 0.4353          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8096 = 1.58 * 1.00 * 6.1918 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7376 = 1.58 * 1.00 * 6.1243 + 1.00 * 0.0412                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.27   18.28    None  None   None       |
|    all(noH): 2823   0      0.00    98.27   18.28    None  None   None       |
|    Sol.    : 438    0      0.00    73.63   36.13    None  None   None       |
|    Mac.    : 2385   0      0.00    98.27   15.00    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:     0.000 -   9.827:  894   |   5:    49.135 -  58.962:   72        |
|      1:     9.827 -  19.654:  856   |   6:    58.962 -  68.789:   22        |
|      2:    19.654 -  29.481:  532   |   7:    68.789 -  78.616:    1        |
|      3:    29.481 -  39.308:  301   |   8:    78.616 -  88.443:    0        |
|      4:    39.308 -  49.135:  144   |   9:    88.443 -  98.270:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3567 r_free = 0.4353             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3565 r_free = 0.4357             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3565   r_free= 0.4357   ksol= 0.26   Bsol= 11.63   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,3.19,-0.73,0.00,-0.00,-0.00); trace/3= 1.03                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.126504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3557   r_free= 0.4327   ksol= 0.32   Bsol= 57.82   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.18,1.98,-0.10,0.00,-0.00,-0.00); trace/3= 0.69                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.126915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.948624             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.777  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.691813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.002   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3557      final r-factor (work) = 0.2839          |
| start r-factor (free) = 0.4327      final r-factor (free) = 0.3444          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.0714 = 16.95 * 0.50 * 6.1256 + 1.00 * 0.1609                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4002 = 16.95 * 0.50 * 6.0487 + 1.00 * 0.1420                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2839      final r-factor (work) = 0.2630          |
| start r-factor (free) = 0.3444      final r-factor (free) = 0.3365          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2551 = 1.69 * 1.00 * 6.0487 + 1.00 * 0.0219                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2227 = 1.69 * 1.00 * 5.9041 + 1.00 * 0.2340                              |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.96   18.52    None  None   None       |
|    all(noH): 2823   0      0.00    85.96   18.52    None  None   None       |
|    Sol.    : 438    0      0.00    74.57   38.05    None  None   None       |
|    Mac.    : 2385   0      0.00    85.96   14.94    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 -   8.596:  738   |   5:    42.979 -  51.575:  118        |
|      1:     8.596 -  17.192:  859   |   6:    51.575 -  60.171:   67        |
|      2:    17.192 -  25.788:  532   |   7:    60.171 -  68.767:   23        |
|      3:    25.788 -  34.383:  290   |   8:    68.767 -  77.363:    3        |
|      4:    34.383 -  42.979:  192   |   9:    77.363 -  85.959:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2630 r_free = 0.3365             target_work(ml) = 5.895         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2628 r_free = 0.3363             target_work(ml) = 5.895         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2628   r_free= 0.3363   ksol= 0.32   Bsol= 57.82   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.18,1.98,-0.10,0.00,-0.00,-0.00); trace/3= 0.69                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.894817                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2631   r_free= 0.3354   ksol= 0.33   Bsol= 64.44   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.71,-0.56,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.893110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.922854              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.679  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 14.129645             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.776   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2631      final r-factor (work) = 0.2255          |
| start r-factor (free) = 0.3354      final r-factor (free) = 0.2821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6272 = 5.92 * 0.50 * 5.9042 + 1.00 * 0.1424                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3531 = 5.92 * 0.50 * 5.8355 + 1.00 * 0.0717                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2255      final r-factor (work) = 0.2037          |
| start r-factor (free) = 0.2821      final r-factor (free) = 0.2671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 82.4771 = 14.13 * 1.00 * 5.8355 + 1.00 * 0.0234                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 80.5967 = 14.13 * 1.00 * 5.7023 + 1.00 * 0.0253                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.57  20.65    None  None   None       |
|    all(noH): 2823   0      0.00    122.57  20.65    None  None   None       |
|    Sol.    : 438    0      2.53    122.57  50.85    None  None   None       |
|    Mac.    : 2385   0      0.00    118.44  15.10    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 -  12.257: 1334   |   5:    61.284 -  73.540:   83        |
|      1:    12.257 -  24.513:  794   |   6:    73.540 -  85.797:   73        |
|      2:    24.513 -  36.770:  231   |   7:    85.797 -  98.054:   29        |
|      3:    36.770 -  49.027:  163   |   8:    98.054 - 110.310:   17        |
|      4:    49.027 -  61.284:   93   |   9:   110.310 - 122.567:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2037 r_free = 0.2671             target_work(ml) = 5.677         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2036 r_free = 0.2669             target_work(ml) = 5.677         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2036   r_free= 0.2669   ksol= 0.33   Bsol= 64.44   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.71,-0.56,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.677119                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2038   r_free= 0.2680   ksol= 0.34   Bsol= 83.62   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,0.26,-0.76,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.678922                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.897850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.429  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2038      final r-factor (work) = 0.1683          |
| start r-factor (free) = 0.2680      final r-factor (free) = 0.2275          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0374 = 4.90 * 0.50 * 5.7028 + 1.00 * 0.0717                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7951 = 4.90 * 0.50 * 5.6036 + 1.00 * 0.0723                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1683      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2275      final r-factor (free) = 0.2068          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8662 = 0.51 * 1.00 * 5.6036 + 1.00 * 0.0255                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7914 = 0.51 * 1.00 * 5.4778 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.37  18.75    None  None   None       |
|    all(noH): 2823   0      0.00    116.37  18.75    None  None   None       |
|    Sol.    : 438    0      4.65    109.37  47.99    None  None   None       |
|    Mac.    : 2385   0      0.00    116.37  13.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.637: 1404   |   5:    58.183 -  69.819:   82        |
|      1:    11.637 -  23.273:  815   |   6:    69.819 -  81.456:   53        |
|      2:    23.273 -  34.910:  206   |   7:    81.456 -  93.093:   25        |
|      3:    34.910 -  46.546:  114   |   8:    93.093 - 104.729:   15        |
|      4:    46.546 -  58.183:  103   |   9:   104.729 - 116.366:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1543 r_free = 0.2068             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1542 r_free = 0.2066             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.2066   ksol= 0.34   Bsol= 83.62   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,0.26,-0.76,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.428627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1545   r_free= 0.2069   ksol= 0.33   Bsol= 76.59   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.41,-0.91,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.429600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.166462              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.494  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267591              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2069      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2252 = 5.17 * 0.50 * 5.4788 + 1.00 * 0.0723                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9633 = 5.17 * 0.50 * 5.3709 + 1.00 * 0.0891                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1790          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4515 = 0.27 * 1.00 * 5.3709 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4289 = 0.27 * 1.00 * 5.2992 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    112.27  17.59    None  None   None       |
|    all(noH): 2823   0      0.98    112.27  17.59    None  None   None       |
|    Sol.    : 438    0      5.08    103.33  44.43    None  None   None       |
|    Mac.    : 2385   0      0.98    112.27  12.66    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:     0.984 -  12.112: 1536   |   5:    56.628 -  67.757:   78        |
|      1:    12.112 -  23.241:  758   |   6:    67.757 -  78.886:   40        |
|      2:    23.241 -  34.370:  159   |   7:    78.886 -  90.015:   23        |
|      3:    34.370 -  45.499:  122   |   8:    90.015 - 101.144:    4        |
|      4:    45.499 -  56.628:   96   |   9:   101.144 - 112.273:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1296 r_free = 0.1790             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1789             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1789   ksol= 0.33   Bsol= 76.59   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.41,-0.91,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.279716                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7076 0.99   1463  166 0.0994 0.1373      5.4163      5.6215|
|  2:  4.7076 -  3.7551 0.99   1397  154 0.0882 0.1151      5.4733      5.6932|
|  3:  3.7551 -  3.2859 0.99   1383  148 0.1172 0.1850       5.553      5.9539|
|  4:  3.2859 -  2.9879 0.99   1364  154 0.1518 0.1830         5.6      5.7461|
|  5:  2.9879 -  2.7752 0.99   1367  152 0.1589 0.2048       5.487      5.6636|
|  6:  2.7752 -  2.6124 0.99   1355  154 0.1530 0.2236      5.3701      5.5803|
|  7:  2.6124 -  2.4822 0.98   1335  140 0.1479 0.1996      5.3025      5.5289|
|  8:  2.4822 -  2.3745 0.98   1343  152 0.1462 0.1830      5.2134      5.3802|
|  9:  2.3745 -  2.2834 0.99   1350  154 0.1410 0.2134      5.1587      5.4063|
| 10:  2.2834 -  2.2049 0.98   1334  149 0.1341 0.1867      5.0935      5.3562|
| 11:  2.2049 -  2.1361 0.97   1334  143 0.1280 0.2030      5.0414       5.307|
| 12:  2.1361 -  2.0752 0.99   1307  149 0.1331 0.2047      4.9904      5.2435|
| 13:  2.0752 -  2.0207 0.76   1037  121 0.1352 0.1822      4.9008      5.0951|
| 14:  2.0207 -  1.9715 0.19    261   23 0.1356 0.1829      4.7761      5.0766|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7076  1463   166  0.93  10.19   0.96     0.94       8577.32|
|  2:  4.7076 -  3.7551  1397   154  0.95   9.03   1.01     0.99      10314.54|
|  3:  3.7551 -  3.2859  1383   148  0.92  13.45   1.03     1.02      12512.56|
|  4:  3.2859 -  2.9879  1364   154  0.89  17.65   1.01     0.99      13990.59|
|  5:  2.9879 -  2.7752  1367   152  0.86  20.23   1.01     0.98      12071.65|
|  6:  2.7752 -  2.6124  1355   154  0.87  19.23   1.00     0.96       9578.97|
|  7:  2.6124 -  2.4822  1335   140  0.88  18.74   0.99     0.96       8236.19|
|  8:  2.4822 -  2.3745  1343   152  0.88  18.88   1.01     0.96       7189.94|
|  9:  2.3745 -  2.2834  1350   154  0.87  18.99   1.01     0.96       6393.25|
| 10:  2.2834 -  2.2049  1334   149  0.88  18.34   0.99     0.94       5782.95|
| 11:  2.2049 -  2.1361  1334   143  0.88  18.88   1.00     0.95       5499.86|
| 12:  2.1361 -  2.0752  1307   149  0.88  19.33   1.00     0.98       5212.97|
| 13:  2.0752 -  2.0207  1037   121  0.87  19.27   1.00     0.99       4253.79|
| 14:  2.0207 -  1.9715   261    23  0.87  19.17   0.99     0.96       3288.60|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3288.60 max =        13990.59 mean =      8465.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.01|
|phase err.(test): min =        0.00 max =           89.17 mean =        16.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1788   ksol= 0.32   Bsol= 70.04   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.81,-1.04,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.281145                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1788   ksol= 0.32   Bsol= 70.04   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.81,-1.04,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.281145                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7076 0.99   1463  166 0.1009 0.1370      5.4292      5.6216|
|  2:  4.7076 -  3.7551 0.99   1397  154 0.0890 0.1147      5.4777      5.6953|
|  3:  3.7551 -  3.2859 0.99   1383  148 0.1176 0.1835      5.5537      5.9475|
|  4:  3.2859 -  2.9879 0.99   1364  154 0.1519 0.1826      5.5997       5.744|
|  5:  2.9879 -  2.7752 0.99   1367  152 0.1590 0.2049      5.4873      5.6653|
|  6:  2.7752 -  2.6124 0.99   1355  154 0.1532 0.2231      5.3705      5.5802|
|  7:  2.6124 -  2.4822 0.98   1335  140 0.1479 0.1997      5.3024      5.5284|
|  8:  2.4822 -  2.3745 0.98   1343  152 0.1460 0.1832      5.2134      5.3813|
|  9:  2.3745 -  2.2834 0.99   1350  154 0.1408 0.2132      5.1581      5.4056|
| 10:  2.2834 -  2.2049 0.98   1334  149 0.1341 0.1869       5.093       5.357|
| 11:  2.2049 -  2.1361 0.97   1334  143 0.1278 0.2030      5.0406      5.3065|
| 12:  2.1361 -  2.0752 0.99   1307  149 0.1331 0.2052      4.9914      5.2455|
| 13:  2.0752 -  2.0207 0.76   1037  121 0.1352 0.1823       4.901      5.0946|
| 14:  2.0207 -  1.9715 0.19    261   23 0.1357 0.1821      4.7752      5.0717|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7076  1463   166  0.93  10.44   0.96     0.94       8768.82|
|  2:  4.7076 -  3.7551  1397   154  0.94   9.10   1.00     0.99      10384.62|
|  3:  3.7551 -  3.2859  1383   148  0.92  13.37   1.02     1.01      12433.91|
|  4:  3.2859 -  2.9879  1364   154  0.89  17.57   1.01     0.98      13902.28|
|  5:  2.9879 -  2.7752  1367   152  0.86  20.20   1.00     0.98      12038.36|
|  6:  2.7752 -  2.6124  1355   154  0.87  19.22   0.99     0.96       9580.34|
|  7:  2.6124 -  2.4822  1335   140  0.88  18.73   0.98     0.95       8239.98|
|  8:  2.4822 -  2.3745  1343   152  0.88  18.88   1.00     0.95       7193.24|
|  9:  2.3745 -  2.2834  1350   154  0.87  18.98   1.00     0.95       6397.67|
| 10:  2.2834 -  2.2049  1334   149  0.88  18.34   0.98     0.93       5781.61|
| 11:  2.2049 -  2.1361  1334   143  0.88  18.86   0.98     0.94       5497.87|
| 12:  2.1361 -  2.0752  1307   149  0.88  19.34   0.98     0.97       5223.22|
| 13:  2.0752 -  2.0207  1037   121  0.87  19.27   0.98     0.97       4252.25|
| 14:  2.0207 -  1.9715   261    23  0.87  19.15   0.98     0.95       3276.46|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3276.46 max =        13902.28 mean =      8472.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.01|
|phase err.(test): min =        0.00 max =           89.23 mean =        16.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.256)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    112.24  17.56    None  None   None       |
|    all(noH): 2823   0      0.95    112.24  17.56    None  None   None       |
|    Sol.    : 438    0      5.04    103.29  44.40    None  None   None       |
|    Mac.    : 2385   0      0.95    112.24  12.63    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:     0.950 -  12.079: 1536   |   5:    56.594 -  67.723:   78        |
|      1:    12.079 -  23.207:  758   |   6:    67.723 -  78.852:   40        |
|      2:    23.207 -  34.336:  159   |   7:    78.852 -  89.981:   23        |
|      3:    34.336 -  45.465:  122   |   8:    89.981 - 101.110:    4        |
|      4:    45.465 -  56.594:   96   |   9:   101.110 - 112.239:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 5.739
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 347 from: 351
   mapped sites are within: 0.704 - 5.739

peak=    8.597 closest distance to " O   HOH Z  41 " =    1.563
peak=    6.734 closest distance to " O   HOH Z 400 " =    1.177
peak=    5.516 closest distance to " O   HOH Z 210 " =    1.545
peak=    5.396 closest distance to " CB  SER A  63 " =    1.374
peak=    5.197 closest distance to " CB  GLN A 223 " =    1.563
peak=    5.014 closest distance to " O  BHOH Z 338 " =    1.083
peak=    4.992 closest distance to " O   HOH Z 111 " =    1.876
peak=    4.864 closest distance to " O   HOH Z  61 " =    1.631
peak=    4.819 closest distance to " O   HOH Z  49 " =    0.987
peak=    4.812 closest distance to " O   HOH Z 404 " =    1.606
peak=    4.738 closest distance to " O   HOH Z  15 " =    2.116
peak=    4.705 closest distance to " O   HOH Z 433 " =    1.931
peak=    4.702 closest distance to " NH2AARG A 102 " =    1.037
peak=    4.687 closest distance to " O   HOH Z 126 " =    2.117
peak=    4.687 closest distance to " O   HOH Z 132 " =    1.659
peak=    4.653 closest distance to " O   HOH Z 117 " =    1.265
peak=    4.628 closest distance to " O   PRO A 198 " =    1.576
peak=    4.605 closest distance to " O   HOH Z 182 " =    1.252
peak=    4.591 closest distance to " O   HOH Z 120 " =    1.128
peak=    4.588 closest distance to " CA  TYR A  30 " =    1.041
peak=    4.572 closest distance to " CG  PRO A  54 " =    1.148
peak=    4.569 closest distance to " O   HOH Z  80 " =    2.259
peak=    4.536 closest distance to " O   HOH Z 418 " =    1.898
peak=    4.529 closest distance to " O   HOH Z 134 " =    1.964
peak=    4.524 closest distance to " O   HOH Z   4 " =    1.179
peak=    4.441 closest distance to " CG  PRO A 213 " =    1.253
peak=    4.438 closest distance to " OE1 GLN A  88 " =    0.946
peak=    4.427 closest distance to " CG1 ILE A  33 " =    1.234
peak=    4.419 closest distance to " O   HOH Z 406 " =    1.556
peak=    4.415 closest distance to " O   HOH Z 234 " =    3.745
peak=    4.412 closest distance to " O   HOH Z 292 " =    1.607
peak=    4.367 closest distance to " O   HOH Z 214 " =    1.334
peak=    4.365 closest distance to " O   HOH Z 394 " =    1.687
peak=    4.351 closest distance to " CA  GLY A 196 " =    1.042
peak=    4.307 closest distance to " O   HOH Z   7 " =    1.237
peak=    4.302 closest distance to " O   HOH Z  47 " =    1.728
peak=    4.278 closest distance to " CE  LYS A 119 " =    1.314
peak=    4.263 closest distance to " O   HOH Z 425 " =    1.743
peak=    4.253 closest distance to " CG  PRO A 280 " =    0.911
peak=    4.246 closest distance to " O   HOH Z  78 " =    1.365
peak=    4.225 closest distance to " O   HOH Z 124 " =    1.195
peak=    4.204 closest distance to " O   HOH Z  68 " =    1.862
peak=    4.196 closest distance to " O   HOH Z 192 " =    1.567
peak=    4.181 closest distance to " CD  ARG A  66 " =    2.851
peak=    4.169 closest distance to " O   HOH Z  97 " =    1.845
peak=    4.158 closest distance to " O   HOH Z 132 " =    1.703
peak=    4.147 closest distance to " O   HOH Z  37 " =    1.089
peak=    4.125 closest distance to " O   HOH Z  44 " =    2.504
peak=    4.110 closest distance to " O   HOH Z 272 " =    1.335
peak=    4.106 closest distance to " O   HOH Z 411 " =    2.831
peak=    4.091 closest distance to " CB  TRP A 179 " =    1.474
peak=    4.067 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.066 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.061 closest distance to " CG2BVAL A  41 " =    1.075
peak=    4.058 closest distance to " O   HOH Z 324 " =    1.506
peak=    4.051 closest distance to " NE2 HIS A 115 " =    1.102
peak=    4.045 closest distance to " OE1 GLN A  11 " =    2.065
peak=    4.038 closest distance to " CB  ASN A 148 " =    1.264
peak=    4.013 closest distance to " O   HOH Z  40 " =    2.206
peak=    4.010 closest distance to " CG2 VAL A  78 " =    1.011
peak=    4.007 closest distance to " CA  ASP A 191 " =    0.890
peak=    4.004 closest distance to " CB  GLN A 194 " =    0.904
peak=    4.001 closest distance to " O   HOH Z 196 " =    2.625
peak=    3.996 closest distance to " O   HOH Z 108 " =    2.476
peak=    3.994 closest distance to " O   HOH Z 243 " =    1.168
peak=    3.986 closest distance to " CG2 THR A 221 " =    1.121
peak=    3.978 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.968 closest distance to " O   HOH Z  83 " =    1.105
peak=    3.952 closest distance to " O   HOH Z 207 " =    2.011
peak=    3.945 closest distance to " CG  PRO A  90 " =    1.250
peak=    3.939 closest distance to " O   ARG A 275 " =    0.787
peak=    3.928 closest distance to " CB  PRO A  54 " =    0.731
peak=    3.925 closest distance to " O   HOH Z 374 " =    2.758
peak=    3.919 closest distance to " O   HOH Z 174 " =    1.537
peak=    3.917 closest distance to " O   HOH Z 232 " =    2.164
peak=    3.915 closest distance to " O   HOH Z 118 " =    2.090
peak=    3.915 closest distance to " CG AARG A 275 " =    1.160
peak=    3.914 closest distance to " O   HOH Z 150 " =    1.877
peak=    3.911 closest distance to " CB  LEU A 228 " =    1.146
peak=    3.903 closest distance to " O   HOH Z 422 " =    1.155
peak=    3.889 closest distance to " O   HOH Z 108 " =    1.362
peak=    3.887 closest distance to " CG2AVAL A 121 " =    2.021
peak=    3.886 closest distance to " O   HOH Z 369 " =    2.075
peak=    3.875 closest distance to " CB  GLN A 183 " =    1.193
peak=    3.869 closest distance to " O   HOH Z 387 " =    2.484
peak=    3.868 closest distance to " O   HOH Z 154 " =    1.433
peak=    3.867 closest distance to " O  BHOH Z 338 " =    1.190
peak=    3.863 closest distance to " O   HOH Z 389 " =    1.818
peak=    3.853 closest distance to " O   HOH Z 431 " =    1.340
peak=    3.843 closest distance to " O   HOH Z 203 " =    1.895
peak=    3.841 closest distance to " O   HOH Z  54 " =    1.721
peak=    3.838 closest distance to " CG1 VAL A 153 " =    1.045
peak=    3.835 closest distance to " O   HOH Z 298 " =    2.071
peak=    3.835 closest distance to " O   HOH Z 104 " =    3.150
peak=    3.832 closest distance to " O   HOH Z 316 " =    3.102
peak=    3.825 closest distance to " O   HOH Z 403 " =    1.942
peak=    3.824 closest distance to " O   HOH Z 301 " =    1.572
peak=    3.817 closest distance to " O   HOH Z 119 " =    2.291
peak=    3.816 closest distance to " O   HOH Z  22 " =    2.261
peak=    3.814 closest distance to " ND1 HIS A  81 " =    1.465
peak=    3.808 closest distance to " O   HOH Z 112 " =    1.501
peak=    3.797 closest distance to " CB  MET A 105 " =    1.160
peak=    3.796 closest distance to " O   HOH Z 350 " =    1.172
peak=    3.796 closest distance to " O   HOH Z 139 " =    3.153
peak=    3.789 closest distance to " O   HOH Z  47 " =    1.684
peak=    3.787 closest distance to " CB  SER A 141 " =    0.968
peak=    3.784 closest distance to " O   HOH Z 377 " =    1.629
peak=    3.777 closest distance to " CG  PRO A 198 " =    1.437
peak=    3.771 closest distance to " O   HOH Z 184 " =    1.429
peak=    3.768 closest distance to " O   HOH Z 265 " =    2.037
peak=    3.766 closest distance to " O   HOH Z  11 " =    1.172
peak=    3.765 closest distance to " CB  ASN A 187 " =    1.228
peak=    3.765 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.757 closest distance to " O   HOH Z 217 " =    1.365
peak=    3.751 closest distance to " O   ALA A 165 " =    1.279
peak=    3.748 closest distance to " O   HOH Z 163 " =    1.857
peak=    3.741 closest distance to " O   HOH Z 437 " =    1.773
peak=    3.738 closest distance to " CD BLYS A 290 " =    1.060
peak=    3.731 closest distance to " O   HOH Z 298 " =    4.347
peak=    3.719 closest distance to " C   SER A  32 " =    1.138
peak=    3.716 closest distance to " CB  TRP A 150 " =    0.991
peak=    3.699 closest distance to " O   HOH Z 432 " =    1.983
peak=    3.699 closest distance to " N   PHE A 130 " =    1.288
peak=    3.689 closest distance to " O   SER A 276 " =    1.156
peak=    3.682 closest distance to " O   HOH Z 154 " =    2.395
peak=    3.675 closest distance to " OD1 ASN A 217 " =    1.813
peak=    3.675 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.668 closest distance to " O   HOH Z 207 " =    1.813
peak=    3.663 closest distance to " CB  GLU A 277 " =    0.900
peak=    3.663 closest distance to " O   HOH Z  39 " =    1.785
peak=    3.646 closest distance to " O   HOH Z 189 " =    2.350
peak=    3.646 closest distance to " CD2 LEU A 297 " =    1.059
peak=    3.626 closest distance to " CB  TYR A 116 " =    1.433
peak=    3.619 closest distance to " O   HOH Z  49 " =    1.998
peak=    3.616 closest distance to " O   HOH Z 128 " =    2.210
peak=    3.613 closest distance to " O   HOH Z 172 " =    5.739
peak=    3.612 closest distance to " O   HOH Z 426 " =    1.383
peak=    3.611 closest distance to " CB  ASP A 140 " =    0.716
peak=    3.610 closest distance to " O   HOH Z   1 " =    3.008
peak=    3.609 closest distance to " O   GLY A  91 " =    1.210
peak=    3.606 closest distance to " O   HOH Z 215 " =    1.438
peak=    3.603 closest distance to " O   HOH Z 327 " =    1.789
peak=    3.601 closest distance to " CE3 TRP A 274 " =    3.685
peak=    3.594 closest distance to " O   GLY A  23 " =    2.457
peak=    3.592 closest distance to " O   HOH Z 149 " =    2.169
peak=    3.590 closest distance to " O   HOH Z 175 " =    3.752
peak=    3.589 closest distance to " NZ  LYS A 117 " =    3.146
peak=    3.589 closest distance to " O   HOH Z 411 " =    1.551
peak=    3.573 closest distance to " NH2 ARG A 156 " =    1.271
peak=    3.570 closest distance to " O   HOH Z 287 " =    1.928
peak=    3.565 closest distance to " CD  LYS A 119 " =    1.274
peak=    3.563 closest distance to " O   HOH Z 247 " =    1.466
peak=    3.561 closest distance to " CG  PRO A 243 " =    1.125
peak=    3.552 closest distance to " O   HOH Z 193 " =    1.854
peak=    3.544 closest distance to " CA  GLU A 152 " =    0.950
peak=    3.533 closest distance to " O   HOH Z  24 " =    2.236
peak=    3.525 closest distance to " CA  ALA A  21 " =    1.499
peak=    3.521 closest distance to " O   HOH Z 352 " =    1.544
peak=    3.521 closest distance to " O   THR A 251 " =    1.321
peak=    3.520 closest distance to " O   HOH Z 418 " =    5.609
peak=    3.520 closest distance to " CB  ASP A 132 " =    3.787
peak=    3.517 closest distance to " CB  GLN A  58 " =    1.009
peak=    3.508 closest distance to " O   HOH Z 139 " =    4.712
peak=    3.507 closest distance to " CG2 VAL A 197 " =    1.334
peak=    3.503 closest distance to " CD2 TRP A 179 " =    1.311
peak=    3.503 closest distance to " O   HOH Z 227 " =    1.840
peak=    3.500 closest distance to " CA  ARG A 156 " =    0.965
peak=    3.497 closest distance to " CB  ASN A 285 " =    0.838
peak=    3.497 closest distance to " CZ  PHE A 218 " =    1.215
peak=    3.494 closest distance to " O   HOH Z 136 " =    1.284
peak=    3.489 closest distance to " CB  ALA A 100 " =    1.580
peak=    3.489 closest distance to " O   HOH Z 410 " =    1.394
peak=    3.485 closest distance to " O   HOH Z  66 " =    2.021
peak=    3.484 closest distance to " O   HOH Z  95 " =    1.797
peak=    3.483 closest distance to " O   HOH Z 272 " =    1.980
peak=    3.478 closest distance to " OD1 ASN A  69 " =    2.343
peak=    3.476 closest distance to " CA  GLY A 241 " =    0.754
peak=    3.475 closest distance to " O   HOH Z 343 " =    2.378
peak=    3.474 closest distance to " O   HOH Z  43 " =    1.675
peak=    3.464 closest distance to " CB  ALA A 256 " =    1.302
peak=    3.463 closest distance to " O   HOH Z  78 " =    2.316
peak=    3.461 closest distance to " O   HOH Z 372 " =    1.187
peak=    3.461 closest distance to " CA  ASP A 124 " =    0.841
peak=    3.461 closest distance to " OG  SER A  97 " =    3.405
peak=    3.447 closest distance to " O   HOH Z  54 " =    1.300
peak=    3.447 closest distance to " CB  PHE A  16 " =    1.411
peak=    3.446 closest distance to " CB  GLU A 128 " =    1.153
peak=    3.442 closest distance to " CA  ARG A 195 " =    1.083
peak=    3.440 closest distance to " O   HOH Z 186 " =    1.157
peak=    3.433 closest distance to " CA  LYS A  48 " =    1.389
peak=    3.432 closest distance to " O   HOH Z 402 " =    1.717
peak=    3.427 closest distance to " O   HOH Z 145 " =    1.928
peak=    3.427 closest distance to " CA  GLN A 223 " =    0.905
peak=    3.426 closest distance to " CB  ARG A 190 " =    1.635
peak=    3.426 closest distance to " O   HOH Z 134 " =    2.078
peak=    3.424 closest distance to " O   HOH Z 344 " =    3.357
peak=    3.423 closest distance to " CB  SER A 276 " =    1.184
peak=    3.416 closest distance to " O   HOH Z 419 " =    2.558
peak=    3.415 closest distance to " O   HOH Z  48 " =    1.860
peak=    3.415 closest distance to " CD  ARG A  56 " =    1.168
peak=    3.413 closest distance to " CB  SER A  62 " =    0.849
peak=    3.411 closest distance to " O   HOH Z 368 " =    2.128
peak=    3.410 closest distance to " O   HOH Z 260 " =    1.357
peak=    3.408 closest distance to " CB  ASP A 124 " =    0.937
peak=    3.406 closest distance to " O   HOH Z  20 " =    2.304
peak=    3.406 closest distance to " O   HOH Z 116 " =    1.777
peak=    3.405 closest distance to " CA  LYS A 166 " =    1.316
peak=    3.403 closest distance to " CG1 ILE A  49 " =    1.616
peak=    3.400 closest distance to " CD1 LEU A 222 " =    0.823
peak=    3.397 closest distance to " O   HOH Z 336 " =    1.659
peak=    3.395 closest distance to " CE BMET A  47 " =    1.358
peak=    3.394 closest distance to " O   HOH Z 234 " =    2.035
peak=    3.393 closest distance to " CB  TYR A 169 " =    0.937
peak=    3.389 closest distance to " O   HOH Z 345 " =    3.501
peak=    3.389 closest distance to " CG2 THR A 220 " =    0.747
peak=    3.388 closest distance to " CB  ARG A  79 " =    1.509
peak=    3.388 closest distance to " CA  TRP A 274 " =    1.041
peak=    3.383 closest distance to " O   HOH Z 420 " =    2.048
peak=    3.381 closest distance to " O   HOH Z  88 " =    1.679
peak=    3.380 closest distance to " CA  ALA A 299 " =    1.307
peak=    3.376 closest distance to " O   HOH Z 127 " =    1.124
peak=    3.367 closest distance to " O   HOH Z 133 " =    1.446
peak=    3.364 closest distance to " CA  ALA A 100 " =    1.183
peak=    3.363 closest distance to " CD1 TRP A 274 " =    1.092
peak=    3.362 closest distance to " CD2 LEU A 255 " =    1.389
peak=    3.361 closest distance to " N   TYR A  15 " =    0.905
peak=    3.361 closest distance to " O   HOH Z 423 " =    3.136
peak=    3.359 closest distance to " CB  LEU A 261 " =    1.192
peak=    3.359 closest distance to " O   HOH Z 261 " =    1.545
peak=    3.356 closest distance to " O   HOH Z 155 " =    2.993
peak=    3.351 closest distance to " CD  ARG A 269 " =    0.736
peak=    3.350 closest distance to " CA  ARG A 102 " =    1.268
peak=    3.345 closest distance to " CD  PRO A  54 " =    1.071
peak=    3.341 closest distance to " CB  LEU A  83 " =    0.818
peak=    3.339 closest distance to " CB  TYR A  30 " =    1.118
peak=    3.338 closest distance to " O   HOH Z 301 " =    2.093
peak=    3.332 closest distance to " CB  ASN A 148 " =    1.715
peak=    3.331 closest distance to " CD  LYS A 166 " =    1.382
peak=    3.326 closest distance to " O   HOH Z 180 " =    2.216
peak=    3.325 closest distance to " O   HOH Z  64 " =    2.189
peak=    3.320 closest distance to " CB  GLN A  88 " =    1.076
peak=    3.319 closest distance to " O   HOH Z 416 " =    1.263
peak=    3.319 closest distance to " O   HOH Z 162 " =    1.866
peak=    3.313 closest distance to " O   HOH Z 150 " =    3.405
peak=    3.311 closest distance to " N   HIS A 108 " =    1.914
peak=    3.309 closest distance to " CB  PRO A  54 " =    1.237
peak=    3.305 closest distance to " CA  ILE A 106 " =    0.839
peak=    3.303 closest distance to " OD2 ASP A 286 " =    3.035
peak=    3.302 closest distance to " O   HOH Z  63 " =    1.525
peak=    3.300 closest distance to " O   HOH Z 395 " =    1.341
peak=    3.296 closest distance to " O   HOH Z  21 " =    1.804
peak=    3.296 closest distance to " CG  GLN A  89 " =    1.334
peak=    3.296 closest distance to " NH1 ARG A  56 " =    1.236
peak=    3.295 closest distance to " O   HOH Z 303 " =    2.440
peak=    3.291 closest distance to " OG  SER A 245 " =    1.608
peak=    3.288 closest distance to " NE AARG A 275 " =    1.649
peak=    3.287 closest distance to " OE1 GLN A  58 " =    1.082
peak=    3.287 closest distance to " CD  ARG A 159 " =    0.833
peak=    3.286 closest distance to " C   ASN A 209 " =    1.203
peak=    3.285 closest distance to " O   HOH Z 142 " =    1.587
peak=    3.284 closest distance to " NE2 GLN A 278 " =    2.519
peak=    3.284 closest distance to " O   HOH Z  42 " =    1.469
peak=    3.283 closest distance to " CD  ARG A 195 " =    1.000
peak=    3.277 closest distance to " CD1 PHE A  59 " =    1.726
peak=    3.269 closest distance to " CB  ILE A 234 " =    0.972
peak=    3.268 closest distance to " CB  SER A   3 " =    1.659
peak=    3.268 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.267 closest distance to " N   ASN A  39 " =    1.234
peak=    3.261 closest distance to " O   HOH Z 132 " =    2.169
peak=    3.261 closest distance to " O   HOH Z 142 " =    1.543
peak=    3.261 closest distance to " OG  SER A  62 " =    3.262
peak=    3.258 closest distance to " O   HOH Z 327 " =    2.449
peak=    3.258 closest distance to " NH2BARG A 145 " =    1.231
peak=    3.254 closest distance to " CB  ALA A 154 " =    1.267
peak=    3.252 closest distance to " O   HOH Z 427 " =    1.152
peak=    3.247 closest distance to " O   HOH Z  14 " =    1.786
peak=    3.246 closest distance to " CA  THR A 294 " =    1.787
peak=    3.244 closest distance to " CB  ARG A 259 " =    1.820
peak=    3.241 closest distance to " O   HOH Z  44 " =    2.863
peak=    3.241 closest distance to " CA  ARG A 139 " =    1.424
peak=    3.239 closest distance to " O   HOH Z 279 " =    2.445
peak=    3.237 closest distance to " CG  GLN A  58 " =    2.293
peak=    3.234 closest distance to " CB  SER A  26 " =    0.901
peak=    3.230 closest distance to " O   HOH Z 259 " =    1.808
peak=    3.225 closest distance to " CA  ALA A 160 " =    0.993
peak=    3.224 closest distance to " CE  MET A 188 " =    1.640
peak=    3.223 closest distance to " C   VAL A 265 " =    1.239
peak=    3.220 closest distance to " CA  GLY A  75 " =    1.204
peak=    3.220 closest distance to " CA  SER A  87 " =    0.844
peak=    3.220 closest distance to " O   HOH Z 130 " =    3.690
peak=    3.219 closest distance to " O   HOH Z 245 " =    1.390
peak=    3.219 closest distance to " O   HOH Z 362 " =    3.049
peak=    3.215 closest distance to " CA  ARG A  36 " =    1.115
peak=    3.212 closest distance to " O   HOH Z 281 " =    4.054
peak=    3.211 closest distance to " CA  VAL A  41 " =    0.798
peak=    3.210 closest distance to " CB  MET A  47 " =    1.039
peak=    3.210 closest distance to " O   HOH Z 200 " =    2.332
peak=    3.209 closest distance to " CE2 TYR A 186 " =    0.975
peak=    3.204 closest distance to " CA  LEU A 282 " =    1.062
peak=    3.204 closest distance to " O   HOH Z 313 " =    2.135
peak=    3.200 closest distance to " CG2 ILE A  20 " =    1.175
peak=    3.197 closest distance to " CZ3 TRP A  85 " =    0.958
peak=    3.195 closest distance to " OE1 GLN A  77 " =    0.753
peak=    3.195 closest distance to " CA  ASP A 149 " =    1.464
peak=    3.190 closest distance to " CB  ASN A 170 " =    1.260
peak=    3.187 closest distance to " CB  VAL A 265 " =    1.356
peak=    3.187 closest distance to " O   HOH Z  19 " =    2.276
peak=    3.186 closest distance to " CG  GLN A  77 " =    0.767
peak=    3.186 closest distance to " OG  SER A 276 " =    0.704
peak=    3.185 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.182 closest distance to " O   HOH Z 171 " =    3.845
peak=    3.173 closest distance to " O   HOH Z  33 " =    1.875
peak=    3.166 closest distance to " CD  PRO A 280 " =    1.070
peak=    3.166 closest distance to " O   HOH Z 130 " =    1.214
peak=    3.162 closest distance to " CG2 THR A  42 " =    0.925
peak=    3.158 closest distance to " N   SER A 164 " =    0.952
peak=    3.152 closest distance to " O   HOH Z 115 " =    1.917
peak=    3.146 closest distance to " CH2 TRP A 274 " =    2.268
peak=    3.142 closest distance to " OD1 ASN A 215 " =    1.196
peak=    3.139 closest distance to " NZ  LYS A 166 " =    3.288
peak=    3.137 closest distance to " CD2 PHE A  59 " =    1.810
peak=    3.137 closest distance to " CG  LEU A 167 " =    1.063
peak=    3.134 closest distance to " O   HOH Z 409 " =    2.993
peak=    3.134 closest distance to " CA  LEU A  83 " =    1.611
peak=    3.129 closest distance to " O   HOH Z 435 " =    1.848
peak=    3.127 closest distance to " CB  THR A 235 " =    1.215
peak=    3.122 closest distance to " O   HOH Z 185 " =    1.879
peak=    3.121 closest distance to " O   HOH Z  57 " =    2.087
peak=    3.118 closest distance to " CB  ASP A 253 " =    1.100
peak=    3.111 closest distance to " O   HOH Z 353 " =    2.659
peak=    3.110 closest distance to " CB  VAL A 296 " =    1.498
peak=    3.096 closest distance to " CA  ALA A 295 " =    1.000
peak=    3.094 closest distance to " CB  ILE A 199 " =    0.969
peak=    3.088 closest distance to " O   HOH Z 195 " =    1.388
peak=    3.088 closest distance to " CB  TYR A 247 " =    1.062
peak=    3.086 closest distance to " O   HOH Z 284 " =    2.892
peak=    3.086 closest distance to " O   HOH Z 102 " =    1.380
peak=    3.086 closest distance to " NE AARG A 102 " =    1.346
peak=    3.084 closest distance to " O   HOH Z 358 " =    1.448
peak=    3.083 closest distance to " O   HOH Z 379 " =    1.494
peak=    3.077 closest distance to " O   HOH Z 164 " =    1.907
peak=    3.070 closest distance to " N   TYR A 116 " =    1.924
peak=    3.060 closest distance to " CB  ALA A 248 " =    1.083
peak=    3.052 closest distance to " O   HOH Z 371 " =    2.968
peak=    3.050 closest distance to " O   ASN A  74 " =    1.571
peak=    3.026 closest distance to " CZ  PHE A 192 " =    0.975
peak=    3.011 closest distance to " O   HOH Z 237 " =    1.898

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 231         
Filter by distance & map next to the model:
   mapped sites are within: 0.423 - 5.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 231
   mapped sites are within: 0.712 - 5.853

peak=   -4.868 closest distance to " N   ARG A 275 " =    0.872
peak=   -4.540 closest distance to " O   HOH Z 166 " =    1.713
peak=   -4.268 closest distance to " O   HOH Z 184 " =    1.119
peak=   -4.256 closest distance to " O   HOH Z  13 " =    1.625
peak=   -4.241 closest distance to " O   HOH Z 128 " =    4.366
peak=   -4.222 closest distance to " O   HOH Z 400 " =    1.045
peak=   -4.192 closest distance to " C   ASN A 285 " =    2.660
peak=   -4.181 closest distance to " O   HOH Z  58 " =    0.715
peak=   -4.173 closest distance to " O   HOH Z 350 " =    0.857
peak=   -4.169 closest distance to " CD  GLN A  88 " =    0.826
peak=   -4.098 closest distance to " O   HOH Z  19 " =    2.058
peak=   -4.069 closest distance to " N   ALA A  43 " =    2.675
peak=   -4.062 closest distance to " OG1 THR A  82 " =    1.895
peak=   -4.050 closest distance to " O   HOH Z 411 " =    4.481
peak=   -4.047 closest distance to " O   HOH Z 290 " =    0.990
peak=   -4.023 closest distance to " CB  LEU A 167 " =    2.115
peak=   -4.011 closest distance to " CD1 PHE A  59 " =    1.921
peak=   -3.997 closest distance to " CA  GLU A 277 " =    1.094
peak=   -3.982 closest distance to " OG  SER A  97 " =    2.268
peak=   -3.976 closest distance to " O   HOH Z 151 " =    1.508
peak=   -3.972 closest distance to " CD  GLN A 223 " =    1.031
peak=   -3.962 closest distance to " O   HOH Z  37 " =    1.373
peak=   -3.951 closest distance to " CD2 LEU A 237 " =    2.552
peak=   -3.948 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.944 closest distance to " O   HOH Z  38 " =    0.772
peak=   -3.928 closest distance to " O   HOH Z  83 " =    1.392
peak=   -3.927 closest distance to " C   TRP A 274 " =    1.007
peak=   -3.912 closest distance to " OD2 ASP A 171 " =    2.265
peak=   -3.909 closest distance to " CG2 ILE A  49 " =    2.590
peak=   -3.885 closest distance to " O   HOH Z 377 " =    1.929
peak=   -3.874 closest distance to " CA  VAL A  67 " =    2.917
peak=   -3.820 closest distance to " CA  GLY A 203 " =    2.305
peak=   -3.809 closest distance to " CD2 PHE A  59 " =    2.228
peak=   -3.791 closest distance to " O   HOH Z 109 " =    3.417
peak=   -3.768 closest distance to " CA  ASN A 148 " =    1.726
peak=   -3.762 closest distance to " O   HOH Z 325 " =    1.570
peak=   -3.754 closest distance to " OH  TYR A 169 " =    0.954
peak=   -3.753 closest distance to " O   SER A 276 " =    1.795
peak=   -3.742 closest distance to " NH2 ARG A  66 " =    1.073
peak=   -3.739 closest distance to " O   HOH Z 231 " =    1.798
peak=   -3.727 closest distance to " O   HOH Z  52 " =    1.715
peak=   -3.717 closest distance to " N   GLN A  58 " =    1.664
peak=   -3.705 closest distance to " O   HOH Z  91 " =    2.127
peak=   -3.688 closest distance to " OD2 ASP A 298 " =    0.968
peak=   -3.677 closest distance to " O   HOH Z 221 " =    1.323
peak=   -3.677 closest distance to " CG  GLN A  58 " =    1.135
peak=   -3.669 closest distance to " C   SER A 271 " =    1.228
peak=   -3.662 closest distance to " O   HOH Z  11 " =    1.120
peak=   -3.658 closest distance to " CB  ALA A 161 " =    2.759
peak=   -3.649 closest distance to " O   HOH Z 146 " =    0.712
peak=   -3.646 closest distance to " SG  CYS A 254 " =    3.345
peak=   -3.642 closest distance to " C   GLY A  23 " =    2.313
peak=   -3.639 closest distance to " CB  SER A 276 " =    0.759
peak=   -3.639 closest distance to " CD  ARG A  14 " =    3.254
peak=   -3.634 closest distance to " O   HOH Z 124 " =    1.258
peak=   -3.629 closest distance to " NZ  LYS A 119 " =    1.615
peak=   -3.589 closest distance to " C   THR A 279 " =    1.196
peak=   -3.585 closest distance to " CA  SER A 164 " =    2.192
peak=   -3.582 closest distance to " O   HOH Z   5 " =    1.620
peak=   -3.582 closest distance to " O   HOH Z 222 " =    1.162
peak=   -3.579 closest distance to " C   SER A 206 " =    1.476
peak=   -3.576 closest distance to " CE  MET A  93 " =    1.260
peak=   -3.570 closest distance to " O   HOH Z   7 " =    0.900
peak=   -3.569 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.569 closest distance to " O   HOH Z  71 " =    1.491
peak=   -3.563 closest distance to " O   HOH Z 348 " =    2.150
peak=   -3.559 closest distance to " O   TYR A  15 " =    1.480
peak=   -3.547 closest distance to " O   HOH Z 207 " =    1.782
peak=   -3.525 closest distance to " O   VAL A 174 " =    2.100
peak=   -3.525 closest distance to " O   HOH Z 150 " =    1.787
peak=   -3.524 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -3.522 closest distance to " CE  LYS A 119 " =    0.901
peak=   -3.518 closest distance to " O   HOH Z 103 " =    2.140
peak=   -3.518 closest distance to " O   HOH Z 210 " =    0.967
peak=   -3.515 closest distance to " CA  ASN A 127 " =    1.095
peak=   -3.508 closest distance to " CG  ARG A 269 " =    2.537
peak=   -3.504 closest distance to " O   GLY A 118 " =    2.501
peak=   -3.504 closest distance to " NH2 ARG A  66 " =    0.829
peak=   -3.494 closest distance to " O   GLY A 196 " =    1.257
peak=   -3.492 closest distance to " CG2 THR A 221 " =    2.210
peak=   -3.485 closest distance to " C   ASN A 187 " =    1.996
peak=   -3.478 closest distance to " OXT GLY A 302 " =    3.005
peak=   -3.477 closest distance to " O   HOH Z 414 " =    1.394
peak=   -3.471 closest distance to " O   HOH Z 423 " =    1.148
peak=   -3.471 closest distance to " O   HOH Z 281 " =    4.756
peak=   -3.461 closest distance to " O   HOH Z 399 " =    2.375
peak=   -3.456 closest distance to " O   HOH Z 418 " =    1.570
peak=   -3.452 closest distance to " O   HOH Z 234 " =    4.199
peak=   -3.444 closest distance to " O   HOH Z 422 " =    1.052
peak=   -3.443 closest distance to " O   HOH Z  17 " =    1.161
peak=   -3.435 closest distance to " CD2 LEU A 143 " =    2.549
peak=   -3.431 closest distance to " O   HOH Z 117 " =    0.885
peak=   -3.420 closest distance to " O   HOH Z 186 " =    1.361
peak=   -3.419 closest distance to " ND2 ASN A  45 " =    1.886
peak=   -3.415 closest distance to " O   HOH Z 292 " =    1.479
peak=   -3.414 closest distance to " OD2 ASP A 171 " =    1.905
peak=   -3.406 closest distance to " O   HOH Z 198 " =    1.665
peak=   -3.400 closest distance to " CB  SER A 146 " =    2.059
peak=   -3.397 closest distance to " CH2 TRP A 179 " =    1.099
peak=   -3.395 closest distance to " O   HOH Z 389 " =    2.123
peak=   -3.394 closest distance to " OD1 ASP A 171 " =    1.368
peak=   -3.390 closest distance to " CB  ALA A  43 " =    2.644
peak=   -3.386 closest distance to " CB  ASN A 170 " =    2.173
peak=   -3.384 closest distance to " O   HOH Z 426 " =    2.088
peak=   -3.376 closest distance to " CD2 HIS A 115 " =    1.041
peak=   -3.375 closest distance to " O   PHE A 218 " =    1.346
peak=   -3.375 closest distance to " OE1 GLN A  88 " =    0.957
peak=   -3.370 closest distance to " CA  TYR A  68 " =    2.920
peak=   -3.367 closest distance to " CB  PRO A 243 " =    2.713
peak=   -3.364 closest distance to " O   HOH Z 388 " =    1.931
peak=   -3.363 closest distance to " O   HOH Z 111 " =    1.259
peak=   -3.363 closest distance to " OG  SER A  62 " =    4.898
peak=   -3.363 closest distance to " CD2 TRP A 274 " =    2.326
peak=   -3.361 closest distance to " C   HIS A 108 " =    1.130
peak=   -3.358 closest distance to " O   HOH Z   7 " =    1.483
peak=   -3.357 closest distance to " O   HOH Z 231 " =    1.454
peak=   -3.351 closest distance to " CB  ALA A  10 " =    1.920
peak=   -3.351 closest distance to " O   HOH Z 275 " =    1.698
peak=   -3.350 closest distance to " O   HOH Z 396 " =    1.486
peak=   -3.348 closest distance to " ND2 ASN A 127 " =    1.473
peak=   -3.346 closest distance to " OG ASER A  12 " =    1.672
peak=   -3.343 closest distance to " N   LEU A 261 " =    1.182
peak=   -3.342 closest distance to " CA  GLY A 133 " =    2.475
peak=   -3.341 closest distance to " OG  SER A  26 " =    1.248
peak=   -3.341 closest distance to " CH2 TRP A 177 " =    2.064
peak=   -3.337 closest distance to " O   HOH Z  95 " =    0.795
peak=   -3.332 closest distance to " SD  MET A  93 " =    2.436
peak=   -3.329 closest distance to " O   HOH Z 157 " =    3.581
peak=   -3.326 closest distance to " O   HOH Z 221 " =    1.343
peak=   -3.325 closest distance to " N   SER A 134 " =    1.219
peak=   -3.323 closest distance to " O   SER A 135 " =    1.848
peak=   -3.322 closest distance to " CE2 PHE A  38 " =    1.896
peak=   -3.321 closest distance to " CA  HIS A  86 " =    2.220
peak=   -3.320 closest distance to " OD1 ASP A 191 " =    2.030
peak=   -3.315 closest distance to " O   HOH Z 310 " =    1.088
peak=   -3.314 closest distance to " O   TYR A 186 " =    2.538
peak=   -3.314 closest distance to " CA  SER A 276 " =    1.445
peak=   -3.313 closest distance to " CD2 PHE A  61 " =    1.798
peak=   -3.311 closest distance to " O   HOH Z 313 " =    1.344
peak=   -3.304 closest distance to " CG  TRP A 266 " =    1.811
peak=   -3.300 closest distance to " N   ALA A 226 " =    2.100
peak=   -3.300 closest distance to " CE2 TYR A  30 " =    2.620
peak=   -3.298 closest distance to " O   VAL A 125 " =    2.084
peak=   -3.294 closest distance to " O   HOH Z 137 " =    1.411
peak=   -3.293 closest distance to " O   HOH Z 185 " =    2.429
peak=   -3.291 closest distance to " CG  MET A 105 " =    0.923
peak=   -3.290 closest distance to " NH1AARG A 275 " =    1.561
peak=   -3.281 closest distance to " CD2 LEU A 167 " =    1.871
peak=   -3.275 closest distance to " CB  CYS A 254 " =    2.251
peak=   -3.268 closest distance to " CG  PRO A 243 " =    1.550
peak=   -3.267 closest distance to " CG  LEU A  83 " =    2.081
peak=   -3.266 closest distance to " O   HOH Z 422 " =    1.768
peak=   -3.261 closest distance to " CA  VAL A 232 " =    2.423
peak=   -3.260 closest distance to " CG  LYS A 166 " =    1.959
peak=   -3.260 closest distance to " O   HOH Z 120 " =    0.965
peak=   -3.259 closest distance to " CD1 TYR A 247 " =    2.299
peak=   -3.258 closest distance to " SG ACYS A 201 " =    2.091
peak=   -3.253 closest distance to " CD  ARG A 156 " =    2.067
peak=   -3.247 closest distance to " O   HOH Z  22 " =    1.937
peak=   -3.245 closest distance to " NH2 ARG A 156 " =    1.202
peak=   -3.244 closest distance to " O   HOH Z  60 " =    2.315
peak=   -3.243 closest distance to " O   HOH Z 213 " =    1.542
peak=   -3.239 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.239 closest distance to " CB  PRO A 163 " =    2.706
peak=   -3.228 closest distance to " O   ALA A   1 " =    2.044
peak=   -3.226 closest distance to " CA  ALA A  34 " =    2.467
peak=   -3.224 closest distance to " O   HOH Z 283 " =    2.146
peak=   -3.221 closest distance to " CD2 LEU A 300 " =    2.738
peak=   -3.220 closest distance to " O   HOH Z 351 " =    1.750
peak=   -3.220 closest distance to " ND2 ASN A  45 " =    1.061
peak=   -3.220 closest distance to " O   HOH Z 118 " =    5.853
peak=   -3.216 closest distance to " OE1 GLN A  73 " =    0.894
peak=   -3.214 closest distance to " OD1 ASN A  39 " =    2.261
peak=   -3.213 closest distance to " ND2 ASN A 252 " =    1.835
peak=   -3.212 closest distance to " CG  ARG A 219 " =    2.384
peak=   -3.208 closest distance to " CB  ARG A 219 " =    2.654
peak=   -3.207 closest distance to " CA  VAL A 197 " =    0.941
peak=   -3.203 closest distance to " O   HOH Z 215 " =    3.381
peak=   -3.198 closest distance to " CD1 TRP A 179 " =    1.053
peak=   -3.198 closest distance to " N   ILE A 120 " =    1.100
peak=   -3.193 closest distance to " O   HOH Z  69 " =    2.014
peak=   -3.190 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.190 closest distance to " O   HOH Z 416 " =    0.801
peak=   -3.187 closest distance to " O   HOH Z 251 " =    1.652
peak=   -3.179 closest distance to " ND2 ASN A  60 " =    2.062
peak=   -3.177 closest distance to " O   HOH Z 136 " =    1.680
peak=   -3.176 closest distance to " O   HOH Z 166 " =    2.447
peak=   -3.171 closest distance to " C   GLN A 240 " =    2.332
peak=   -3.166 closest distance to " O   HOH Z 402 " =    1.173
peak=   -3.165 closest distance to " O   LEU A 143 " =    1.317
peak=   -3.164 closest distance to " OE1 GLU A 277 " =    2.200
peak=   -3.163 closest distance to " O   HOH Z 298 " =    3.025
peak=   -3.162 closest distance to " N   THR A 157 " =    1.818
peak=   -3.160 closest distance to " O   HOH Z 182 " =    2.707
peak=   -3.156 closest distance to " SG  CYS A 168 " =    1.017
peak=   -3.155 closest distance to " CG  GLU A  53 " =    1.405
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.064
peak=   -3.151 closest distance to " CG  PHE A 225 " =    1.268
peak=   -3.151 closest distance to " CE2 PHE A  61 " =    2.467
peak=   -3.151 closest distance to " CB  ALA A 291 " =    2.308
peak=   -3.149 closest distance to " O   HOH Z 134 " =    2.150
peak=   -3.146 closest distance to " O   HOH Z 380 " =    4.214
peak=   -3.139 closest distance to " O   HOH Z 182 " =    0.888
peak=   -3.139 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.138 closest distance to " O   HOH Z 186 " =    3.608
peak=   -3.136 closest distance to " ND2 ASN A  60 " =    1.816
peak=   -3.135 closest distance to " O   HOH Z 267 " =    1.622
peak=   -3.127 closest distance to " CB  PHE A  16 " =    2.498
peak=   -3.127 closest distance to " O   HOH Z 118 " =    1.039
peak=   -3.127 closest distance to " O   MET A  47 " =    2.491
peak=   -3.127 closest distance to " NE2 HIS A  86 " =    1.017
peak=   -3.120 closest distance to " CZ  ARG A  79 " =    1.764
peak=   -3.115 closest distance to " NH1 ARG A 195 " =    0.948
peak=   -3.109 closest distance to " O   THR A  18 " =    1.504
peak=   -3.108 closest distance to " CB  ALA A 248 " =    2.117
peak=   -3.107 closest distance to " O   HOH Z  39 " =    1.747
peak=   -3.107 closest distance to " CA  GLY A 241 " =    3.054
peak=   -3.089 closest distance to " OG BSER A 134 " =    1.885
peak=   -3.083 closest distance to " O   HOH Z  24 " =    2.169
peak=   -3.083 closest distance to " CD2 PHE A 130 " =    2.972
peak=   -3.073 closest distance to " O   ALA A  10 " =    1.851
peak=   -3.067 closest distance to " CE  MET A 105 " =    2.166
peak=   -3.057 closest distance to " CB  ALA A 227 " =    2.380
peak=   -3.044 closest distance to " O   HOH Z 378 " =    1.253

================= 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    :  0.4884 0.4711   6.296714e+00   6.280726e+00
   1_bss:  0.4823 0.4630   6.293894e+00   6.274113e+00
   1_xyz:  0.3887 0.4299   6.164116e+00   6.222878e+00
   1_adp:  0.3567 0.4353   6.127206e+00   6.226119e+00
   1_occ:  0.3565 0.4357   6.126504e+00   6.226582e+00
   2_bss:  0.3557 0.4327   6.126915e+00   6.224301e+00
   2_xyz:  0.2839 0.3444   5.936487e+00   6.084323e+00
   2_adp:  0.2630 0.3365   5.895302e+00   6.068312e+00
   2_occ:  0.2628 0.3363   5.894817e+00   6.068006e+00
   3_bss:  0.2631 0.3354   5.893110e+00   6.066290e+00
   3_xyz:  0.2255 0.2821   5.750056e+00   5.926536e+00
   3_adp:  0.2037 0.2671   5.677330e+00   5.880505e+00
   3_occ:  0.2036 0.2669   5.677119e+00   5.880085e+00
   4_bss:  0.2038 0.2680   5.678922e+00   5.882693e+00
   4_xyz:  0.1683 0.2275   5.505901e+00   5.733857e+00
   4_adp:  0.1543 0.2068   5.429481e+00   5.647004e+00
   4_occ:  0.1542 0.2066   5.428627e+00   5.645896e+00
   5_bss:  0.1545 0.2069   5.429600e+00   5.646122e+00
   5_xyz:  0.1336 0.1865   5.307555e+00   5.543374e+00
   5_adp:  0.1296 0.1790   5.280183e+00   5.509266e+00
   5_occ:  0.1294 0.1789   5.279716e+00   5.509029e+00
   5_bss:  0.1298 0.1788   5.281145e+00   5.508747e+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:  0.264  11.627   0.634   3.186  -0.733   0.000  -0.000  -0.000
   1_xyz:  0.264  11.627   0.634   3.186  -0.733   0.000  -0.000  -0.000
   1_adp:  0.264  11.627   0.634   3.186  -0.733   0.000  -0.000  -0.000
   1_occ:  0.264  11.627   0.634   3.186  -0.733   0.000  -0.000  -0.000
   2_bss:  0.319  57.819   0.183   1.984  -0.099   0.000  -0.000  -0.000
   2_xyz:  0.319  57.819   0.183   1.984  -0.099   0.000  -0.000  -0.000
   2_adp:  0.319  57.819   0.183   1.984  -0.099   0.000  -0.000  -0.000
   2_occ:  0.319  57.819   0.183   1.984  -0.099   0.000  -0.000  -0.000
   3_bss:  0.329  64.444  -0.441   0.710  -0.565   0.000  -0.000  -0.000
   3_xyz:  0.329  64.444  -0.441   0.710  -0.565   0.000  -0.000  -0.000
   3_adp:  0.329  64.444  -0.441   0.710  -0.565   0.000  -0.000  -0.000
   3_occ:  0.329  64.444  -0.441   0.710  -0.565   0.000  -0.000  -0.000
   4_bss:  0.336  83.617  -0.700   0.259  -0.761   0.000  -0.000  -0.000
   4_xyz:  0.336  83.617  -0.700   0.259  -0.761   0.000  -0.000  -0.000
   4_adp:  0.336  83.617  -0.700   0.259  -0.761   0.000  -0.000  -0.000
   4_occ:  0.336  83.617  -0.700   0.259  -0.761   0.000  -0.000  -0.000
   5_bss:  0.332  76.588  -1.134  -0.415  -0.913  -0.000  -0.000  -0.000
   5_xyz:  0.332  76.588  -1.134  -0.415  -0.913  -0.000  -0.000  -0.000
   5_adp:  0.332  76.588  -1.134  -0.415  -0.913  -0.000  -0.000  -0.000
   5_occ:  0.332  76.588  -1.134  -0.415  -0.913  -0.000  -0.000  -0.000
   5_bss:  0.325  70.036  -1.319  -0.809  -1.045  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.228 0.4171  0.5662    73902.735
   1_bss:  57.610 0.4235  0.5956    71088.852
   1_xyz:  49.976 0.5199  0.7193    55720.575
   1_adp:  50.865 0.5078  0.7029    56246.092
   1_occ:  50.895 0.5073  0.7020    56285.221
   2_bss:  50.630 0.5106  0.7019    55764.879
   2_xyz:  38.063 0.6642  0.8835    33666.722
   2_adp:  36.763 0.6798  0.8946    32240.436
   2_occ:  36.747 0.6801  0.8944    32205.092
   3_bss:  36.563 0.6820  0.8729    31853.729
   3_xyz:  29.589 0.7610  0.9423    21619.379
   3_adp:  27.438 0.7851  0.9403    19310.990
   3_occ:  27.425 0.7853  0.9403    19305.474
   4_bss:  27.482 0.7848  0.9305    19432.424
   4_xyz:  22.883 0.8315  0.9675    13476.110
   4_adp:  20.293 0.8583  0.9727    11307.947
   4_occ:  20.265 0.8586  0.9728    11280.629
   5_bss:  20.261 0.8586  0.9590    11287.075
   5_xyz:  17.777 0.8819  0.9733     8972.442
   5_adp:  16.941 0.8900  0.9710     8468.719
   5_occ:  16.929 0.8901  0.9709     8464.873
   5_bss:  16.937 0.8900  0.9622     8472.000
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8898e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8898e-01
   1_xyz:   1.733  0.013  0.107 16.197  0.006  4.105   1.6085e-01
   1_adp:   1.733  0.013  0.107 16.197  0.006  4.105   1.6085e-01
   1_occ:   1.733  0.013  0.107 16.197  0.006  4.105   1.6085e-01
   2_bss:   1.733  0.013  0.107 16.197  0.006  4.105   1.6085e-01
   2_xyz:   1.590  0.013  0.104 15.905  0.007  4.122   1.4200e-01
   2_adp:   1.590  0.013  0.104 15.905  0.007  4.122   1.4200e-01
   2_occ:   1.590  0.013  0.104 15.905  0.007  4.122   1.4200e-01
   3_bss:   1.590  0.013  0.104 15.905  0.007  4.122   1.4200e-01
   3_xyz:   1.146  0.008  0.075 14.969  0.004  4.127   7.1655e-02
   3_adp:   1.146  0.008  0.075 14.969  0.004  4.127   7.1655e-02
   3_occ:   1.146  0.008  0.075 14.969  0.004  4.127   7.1655e-02
   4_bss:   1.146  0.008  0.075 14.969  0.004  4.127   7.1655e-02
   4_xyz:   1.122  0.009  0.077 14.622  0.004  4.116   7.2297e-02
   4_adp:   1.122  0.009  0.077 14.622  0.004  4.116   7.2297e-02
   4_occ:   1.122  0.009  0.077 14.622  0.004  4.116   7.2297e-02
   5_bss:   1.122  0.009  0.077 14.622  0.004  4.116   7.2297e-02
   5_xyz:   1.244  0.012  0.085 14.928  0.004  4.128   8.9070e-02
   5_adp:   1.244  0.012  0.085 14.928  0.004  4.128   8.9070e-02
   5_occ:   1.244  0.012  0.085 14.928  0.004  4.128   8.9070e-02
   5_bss:   1.244  0.012  0.085 14.928  0.004  4.128   8.9070e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.245   2.4489e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.245   2.4489e-01
   1_xyz:  11.228  0.075  0.425 89.023  0.032  1.873   1.0853e-01
   1_adp:  11.228  0.075  0.425 89.023  0.032  1.873   1.0853e-01
   1_occ:  11.228  0.075  0.425 89.023  0.032  1.873   1.0853e-01
   2_bss:  11.228  0.075  0.425 89.023  0.032  1.873   1.0853e-01
   2_xyz:   9.335  0.074  0.290 85.432  0.062  2.101   1.2908e-01
   2_adp:   9.335  0.074  0.290 85.432  0.062  2.101   1.2908e-01
   2_occ:   9.335  0.074  0.290 85.432  0.062  2.101   1.2908e-01
   3_bss:   9.335  0.074  0.290 85.432  0.062  2.101   1.2908e-01
   3_xyz:   8.487  0.057  0.266 86.154  0.024  2.133   6.5868e-02
   3_adp:   8.487  0.057  0.266 86.154  0.024  2.133   6.5868e-02
   3_occ:   8.487  0.057  0.266 86.154  0.024  2.133   6.5868e-02
   4_bss:   8.487  0.057  0.266 86.154  0.024  2.133   6.5868e-02
   4_xyz:   7.886  0.052  0.235 84.770  0.029  2.292   5.4895e-02
   4_adp:   7.886  0.052  0.235 84.770  0.029  2.292   5.4895e-02
   4_occ:   7.886  0.052  0.235 84.770  0.029  2.292   5.4895e-02
   5_bss:   7.886  0.052  0.235 84.770  0.029  2.292   5.4895e-02
   5_xyz:   8.066  0.060  0.258 83.099  0.032  2.171   6.5269e-02
   5_adp:   8.066  0.060  0.258 83.099  0.032  2.171   6.5269e-02
   5_occ:   8.066  0.060  0.258 83.099  0.032  2.171   6.5269e-02
   5_bss:   8.066  0.060  0.258 83.099  0.032  2.171   6.5269e-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:  98.27   0.00  18.28  98.27   0.00  15.00  73.63   0.00  36.13
   1_occ:  98.27   0.00  18.28  98.27   0.00  15.00  73.63   0.00  36.13
   2_bss:  98.27   0.00  18.28  98.27   0.00  15.00  73.63   0.00  36.13
   2_xyz:  98.27   0.00  18.28  98.27   0.00  15.00  73.63   0.00  36.13
   2_adp:  85.96   0.00  18.52  85.96   0.00  14.94  74.57   0.00  38.05
   2_occ:  85.96   0.00  18.52  85.96   0.00  14.94  74.57   0.00  38.05
   3_bss:  85.96   0.00  18.52  85.96   0.00  14.94  74.57   0.00  38.05
   3_xyz:  85.96   0.00  18.52  85.96   0.00  14.94  74.57   0.00  38.05
   3_adp: 122.57   0.00  20.65 118.44   0.00  15.10 122.57   2.53  50.85
   3_occ: 122.57   0.00  20.65 118.44   0.00  15.10 122.57   2.53  50.85
   4_bss: 122.57   0.00  20.65 118.44   0.00  15.10 122.57   2.53  50.85
   4_xyz: 122.57   0.00  20.65 118.44   0.00  15.10 122.57   2.53  50.85
   4_adp: 116.37   0.00  18.75 116.37   0.00  13.38 109.37   4.65  47.99
   4_occ: 116.37   0.00  18.75 116.37   0.00  13.38 109.37   4.65  47.99
   5_bss: 116.37   0.00  18.75 116.37   0.00  13.38 109.37   4.65  47.99
   5_xyz: 116.37   0.00  18.75 116.37   0.00  13.38 109.37   4.65  47.99
   5_adp: 112.27   0.98  17.59 112.27   0.98  12.66 103.33   5.08  44.43
   5_occ: 112.27   0.98  17.59 112.27   0.98  12.66 103.33   5.08  44.43
   5_bss: 112.24   0.95  17.56 112.24   0.95  12.63 103.29   5.04  44.40
------------------------------------------------------------------------
 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:    2.143    0.016    0.405
   1_adp:    2.143    0.016    0.405
   1_occ:    2.143    0.016    0.405
   2_bss:    2.143    0.016    0.405
   2_xyz:    1.968    0.039    0.694
   2_adp:    1.968    0.039    0.694
   2_occ:    1.968    0.039    0.694
   3_bss:    1.968    0.039    0.694
   3_xyz:    1.868    0.079    0.788
   3_adp:    1.868    0.079    0.788
   3_occ:    1.868    0.079    0.788
   4_bss:    1.868    0.079    0.788
   4_xyz:    1.829    0.032    0.884
   4_adp:    1.829    0.032    0.884
   4_occ:    1.829    0.032    0.884
   5_bss:    1.829    0.032    0.884
   5_xyz:    1.823    0.051    0.931
   5_adp:    1.823    0.051    0.931
   5_occ:    1.823    0.051    0.931
   5_bss:    1.823    0.051    0.931
------------------------------------------------------------------------

CPU time actual refinement: 315.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/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_1322/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1322/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.28 
  Macro-tasks:
    bulk solvent and scale       = 46.14  
    individual site refinement   = 130.62 
    weights calculation          = 25.59  
    collect and process          = 5.29   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 207.72 
  Micro-tasks:
    mask                            = 2.60   
    f_calc                          = 100.07 
    alpha_beta                      = 6.96   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 107.83 
    fmodel                         = 7.33   
    r_factors                      = 0.33   
    phase_errors                   = 8.38   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 234.68 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.415 micro seconds
Total CPU time: 5.45 minutes
from_scatterers_fft:    645 calls, 99.91 s
gradients_fft:          590 calls, 96.38 s

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

# Date 2008-01-16 Time 06:58:39 PST -0800 (1200495519.83 s)
Start R-work = 0.4884, R-free = 0.4711 (no bulk solvent and anisotropic scale)
Final R-work = 0.1474, R-free = 0.1960 (no bulk solvent and anisotropic scale)

Start R-work = 0.4823, R-free = 0.4630
Final R-work = 0.1298, R-free = 0.1788