# Date 2008-01-16 Time 06:25:22 PST -0800 (1200493522.33 s)
#phil __OFF__

Command line arguments: "../1137.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15284
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1137

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.6953, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99038
Completeness in resolution range: 0.962794
Completeness with d_max=infinity: 0.959869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99038
Completeness in resolution range: 0.962794
Completeness with d_max=infinity: 0.959869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2596 [2132/2157]  1922   210   9.8%
  bin  2:  4.2596 -  3.3933 [2058/2078]  1851   207  10.1%
  bin  3:  3.3933 -  2.9680 [2021/2040]  1816   205  10.1%
  bin  4:  2.9680 -  2.6983 [2006/2036]  1807   199   9.9%
  bin  5:  2.6983 -  2.5058 [2008/2027]  1813   195   9.7%
  bin  6:  2.5058 -  2.3587 [1986/2011]  1778   208  10.5%
  bin  7:  2.3587 -  2.2409 [1973/2001]  1775   198  10.0%
  bin  8:  2.2409 -  2.1437 [1968/2004]  1773   195   9.9%
  bin  9:  2.1437 -  2.0613 [1963/2005]  1769   194   9.9%
  bin 10:  2.0613 -  1.9904 [1474/1987]  1326   148  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2191
        3.04 -     3.66: 4658
        3.66 -     4.28: 9032
        4.28 -     4.90: 12272
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.035 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.035 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.036 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.071 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28161 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_1137/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.69535 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3291   r_free= 0.3283   ksol= 0.00   Bsol= 0.00   scale= 0.964    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.054596                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7512 0.99   1390  155 0.2910 0.2766       6.356      6.3009|
|  2:  4.7512 -  3.7905 0.99   1335  146 0.2616 0.2648      6.4654      6.4392|
|  3:  3.7905 -  3.3170 0.99   1312  144 0.2832 0.2600      6.3399       6.393|
|  4:  3.3170 -  3.0163 0.99   1299  153 0.2929 0.3195      6.2326      6.2342|
|  5:  3.0163 -  2.8016 0.99   1296  140 0.3338 0.3533      6.1223      6.2201|
|  6:  2.8016 -  2.6373 0.99   1288  140 0.3369 0.3469      6.0486      6.0304|
|  7:  2.6373 -  2.5058 0.99   1289  138 0.3637 0.3524      6.0493       6.094|
|  8:  2.5058 -  2.3972 0.98   1256  150 0.3668 0.3169      5.9797       5.896|
|  9:  2.3972 -  2.3052 0.98   1272  144 0.3569 0.3637       5.918      5.9496|
| 10:  2.3052 -  2.2259 1.00   1276  139 0.3705 0.4132      5.9161      5.9746|
| 11:  2.2259 -  2.1565 0.98   1273  136 0.3901 0.3715      5.9008      5.8922|
| 12:  2.1565 -  2.0951 0.98   1253  140 0.3897 0.3873      5.8196      5.8924|
| 13:  2.0951 -  2.0400 1.00   1260  139 0.3896 0.3856      5.7518      5.6583|
| 14:  2.0400 -  1.9904 0.64    831   95 0.3672 0.3861      5.6578      5.6309|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7512  1390   155  0.79  25.70   0.86     0.81      41473.66|
|  2:  4.7512 -  3.7905  1335   146  0.84  22.36   0.97     0.91      46812.86|
|  3:  3.7905 -  3.3170  1312   144  0.79  27.13   0.99     0.93      48130.60|
|  4:  3.3170 -  3.0163  1299   153  0.76  30.17   0.98     0.91      44676.31|
|  5:  3.0163 -  2.8016  1296   140  0.68  37.18   0.97     0.86      39574.47|
|  6:  2.8016 -  2.6373  1288   140  0.68  37.11   1.00     0.87      34039.31|
|  7:  2.6373 -  2.5058  1289   138  0.69  36.25   0.99     0.87      29498.52|
|  8:  2.5058 -  2.3972  1256   150  0.70  35.58   0.98     0.91      25615.15|
|  9:  2.3972 -  2.3052  1272   144  0.69  36.86   1.02     0.90      24533.88|
| 10:  2.3052 -  2.2259  1276   139  0.67  38.66   1.03     0.89      24553.05|
| 11:  2.2259 -  2.1565  1273   136  0.64  40.81   1.05     0.87      24319.33|
| 12:  2.1565 -  2.0951  1253   140  0.65  40.11   1.02     0.89      21640.25|
| 13:  2.0951 -  2.0400  1260   139  0.65  39.88   1.01     0.90      17834.80|
| 14:  2.0400 -  1.9904   831    95  0.69  36.54   1.05     0.92      13530.89|
|alpha:            min =        0.81 max =            0.93 mean =         0.89|
|beta:             min =    13530.89 max =        48130.60 mean =     31819.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.99 mean =        34.42|
|phase err.(test): min =        0.00 max =           89.91 mean =        34.26|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.669891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.568   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732310              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.453   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      203 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1988 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1828 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2830 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4661 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4371 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5600 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6672 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.158 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3291   r_free= 0.3283   ksol= 0.00   Bsol= 0.00   scale= 0.964    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.054596                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3154   r_free= 0.3143   ksol= 0.33   Bsol= 50.00   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,-2.47,-1.63,-0.00,-0.00,-0.00); trace/3= -0.74                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.032737                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.129258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.960   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.219   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3154      final r-factor (work) = 0.1846          |
| start r-factor (free) = 0.3143      final r-factor (free) = 0.2068          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6311 = 4.13 * 0.50 * 6.0396 + 1.00 * 0.1616                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9619 = 4.13 * 0.50 * 5.7612 + 1.00 * 0.0671                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1846      final r-factor (work) = 0.1719          |
| start r-factor (free) = 0.2068      final r-factor (free) = 0.2109          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1904 = 0.38 * 1.00 * 5.7612 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1058 = 0.38 * 1.00 * 5.4903 + 1.00 * 0.0245                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.31   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    63.31   16.59    None  None   None       |
|    Sol.    : 438    0      5.07    63.31   37.61    None  None   None       |
|    Mac.    : 2385   0      0.00    55.12   12.73    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 -   6.331:  258   |   5:    31.653 -  37.984:   96        |
|      1:     6.331 -  12.661: 1185   |   6:    37.984 -  44.314:  104        |
|      2:    12.661 -  18.992:  698   |   7:    44.314 -  50.645:   73        |
|      3:    18.992 -  25.323:  216   |   8:    50.645 -  56.976:   55        |
|      4:    25.323 -  31.653:  114   |   9:    56.976 -  63.306:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1719 r_free = 0.2109             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1715 r_free = 0.2105             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1715   r_free= 0.2105   ksol= 0.33   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,-2.47,-1.63,-0.00,-0.00,-0.00); trace/3= -0.74                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.495435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1692   r_free= 0.2085   ksol= 0.34   Bsol= 58.52   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-3.03,-1.97,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.487355                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.884716              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260316              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.247   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1692      final r-factor (work) = 0.1294          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0024 = 2.88 * 0.50 * 5.5016 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8026 = 2.88 * 0.50 * 5.3679 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4191 = 0.26 * 1.00 * 5.3679 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3665 = 0.26 * 1.00 * 5.2189 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    73.11   17.05    None  None   None       |
|    all(noH): 2823   0      1.23    73.11   17.05    None  None   None       |
|    Sol.    : 438    0      6.08    73.11   38.83    None  None   None       |
|    Mac.    : 2385   0      1.23    71.95   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.233 -   8.421:  574   |   5:    37.172 -  44.359:   97        |
|      1:     8.421 -  15.609: 1315   |   6:    44.359 -  51.547:   95        |
|      2:    15.609 -  22.796:  392   |   7:    51.547 -  58.735:   72        |
|      3:    22.796 -  29.984:  137   |   8:    58.735 -  65.922:   27        |
|      4:    29.984 -  37.172:  103   |   9:    65.922 -  73.110:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1645             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1643             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1643   ksol= 0.34   Bsol= 58.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-3.03,-1.97,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1632   ksol= 0.33   Bsol= 58.52   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.90,-1.81,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.197557                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.330174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.619  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163641              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1400 = 2.33 * 0.50 * 5.2184 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0836 = 2.33 * 0.50 * 5.1676 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8535 = 0.16 * 1.00 * 5.1676 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8497 = 0.16 * 1.00 * 5.1489 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.72    74.82   16.81    None  None   None       |
|    all(noH): 2823   0      1.72    74.82   16.81    None  None   None       |
|    Sol.    : 438    0      2.86    74.82   37.66    None  None   None       |
|    Mac.    : 2385   0      1.72    73.32   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.717 -   9.027:  695   |   5:    38.269 -  45.579:  109        |
|      1:     9.027 -  16.337: 1264   |   6:    45.579 -  52.889:   85        |
|      2:    16.337 -  23.648:  353   |   7:    52.889 -  60.200:   55        |
|      3:    23.648 -  30.958:  128   |   8:    60.200 -  67.510:   13        |
|      4:    30.958 -  38.269:  111   |   9:    67.510 -  74.821:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1566             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1566             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1566   ksol= 0.33   Bsol= 58.52   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.90,-1.81,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1566   ksol= 0.33   Bsol= 58.52   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.80,-1.74,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.407202              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.363  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.313315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.972  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6854 = 1.41 * 0.50 * 5.1486 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6771 = 1.41 * 0.50 * 5.1520 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6213 = 0.31 * 1.00 * 5.1520 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6220 = 0.31 * 1.00 * 5.1514 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    77.55   16.91    None  None   None       |
|    all(noH): 2823   0      1.04    77.55   16.91    None  None   None       |
|    Sol.    : 438    0      4.14    76.50   38.41    None  None   None       |
|    Mac.    : 2385   0      1.04    77.55   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.039 -   8.690:  661   |   5:    39.293 -  46.943:  114        |
|      1:     8.690 -  16.340: 1294   |   6:    46.943 -  54.594:   89        |
|      2:    16.340 -  23.991:  358   |   7:    54.594 -  62.245:   49        |
|      3:    23.991 -  31.642:  127   |   8:    62.245 -  69.896:   12        |
|      4:    31.642 -  39.293:  109   |   9:    69.896 -  77.546:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1581             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1581             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1581   ksol= 0.33   Bsol= 58.52   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.80,-1.74,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154086                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1581   ksol= 0.33   Bsol= 58.52   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.66,-1.59,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154154                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.245170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.605  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.939309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8354 = 2.25 * 0.50 * 5.1517 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8328 = 2.25 * 0.50 * 5.1398 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8358 = 0.94 * 1.00 * 5.1398 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8301 = 0.94 * 1.00 * 5.1323 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    88.29   17.14    None  None   None       |
|    all(noH): 2823   0      0.48    88.29   17.14    None  None   None       |
|    Sol.    : 438    0      5.21    84.09   39.92    None  None   None       |
|    Mac.    : 2385   0      0.48    88.29   12.96    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:     0.478 -   9.259:  872   |   5:    44.384 -  53.165:   98        |
|      1:     9.259 -  18.040: 1218   |   6:    53.165 -  61.946:   73        |
|      2:    18.040 -  26.822:  260   |   7:    61.946 -  70.727:   30        |
|      3:    26.822 -  35.603:  144   |   8:    70.727 -  79.508:   10        |
|      4:    35.603 -  44.384:  111   |   9:    79.508 -  88.290:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1582             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1582             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1582   ksol= 0.33   Bsol= 58.52   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.66,-1.59,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134944                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7512 0.99   1390  155 0.0977 0.1302      5.3779      5.5234|
|  2:  4.7512 -  3.7905 0.99   1335  146 0.0840 0.1086      5.4234      5.6078|
|  3:  3.7905 -  3.3170 0.99   1312  144 0.1031 0.1504      5.4581      5.8532|
|  4:  3.3170 -  3.0163 0.99   1299  153 0.1176 0.1587      5.4499      5.5881|
|  5:  3.0163 -  2.8016 0.99   1296  140 0.1320 0.1847      5.3211      5.5787|
|  6:  2.8016 -  2.6373 0.99   1288  140 0.1187 0.1706      5.2059      5.4235|
|  7:  2.6373 -  2.5058 0.99   1289  138 0.1236 0.1601      5.1664      5.3698|
|  8:  2.5058 -  2.3972 0.98   1256  150 0.1109 0.1810      5.0226       5.372|
|  9:  2.3972 -  2.3052 0.98   1272  144 0.1129 0.1686       5.011      5.2988|
| 10:  2.3052 -  2.2259 1.00   1276  139 0.1062 0.1802      4.9322      5.2532|
| 11:  2.2259 -  2.1565 0.98   1273  136 0.1114 0.1765      4.9586      5.2761|
| 12:  2.1565 -  2.0951 0.98   1253  140 0.1092 0.1667       4.882      5.1458|
| 13:  2.0951 -  2.0400 1.00   1260  139 0.1130 0.1802      4.7921      5.1012|
| 14:  2.0400 -  1.9904 0.64    831   95 0.1019 0.1658      4.6554      4.9097|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7512  1390   155  0.94   8.92   0.97     0.95       7013.08|
|  2:  4.7512 -  3.7905  1335   146  0.95   7.98   1.01     1.00       8872.78|
|  3:  3.7905 -  3.3170  1312   144  0.94  11.01   1.02     1.02      10034.84|
|  4:  3.3170 -  3.0163  1299   153  0.92  13.44   1.00     0.98      10285.91|
|  5:  3.0163 -  2.8016  1296   140  0.90  16.24   0.99     0.97       8394.26|
|  6:  2.8016 -  2.6373  1288   140  0.90  15.74   0.98     0.96       7182.57|
|  7:  2.6373 -  2.5058  1289   138  0.91  15.57   0.99     0.97       6331.18|
|  8:  2.5058 -  2.3972  1256   150  0.91  14.88   0.98     0.95       4905.73|
|  9:  2.3972 -  2.3052  1272   144  0.91  14.69   0.99     0.95       4751.56|
| 10:  2.3052 -  2.2259  1276   139  0.91  15.29   0.99     0.96       4250.34|
| 11:  2.2259 -  2.1565  1273   136  0.90  16.33   0.98     0.93       4545.02|
| 12:  2.1565 -  2.0951  1253   140  0.91  15.29   1.00     0.99       4102.40|
| 13:  2.0951 -  2.0400  1260   139  0.90  16.48   0.98     0.97       3442.16|
| 14:  2.0400 -  1.9904   831    95  0.92  14.54   0.96     0.92       2568.45|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2568.45 max =        10285.91 mean =      6320.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.59 mean =        13.95|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1582   ksol= 0.32   Bsol= 55.31   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.42,-1.36,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134850                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1582   ksol= 0.32   Bsol= 55.31   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.42,-1.36,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134850                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7512 0.99   1390  155 0.0972 0.1301      5.3734      5.5217|
|  2:  4.7512 -  3.7905 0.99   1335  146 0.0839 0.1085      5.4224      5.6069|
|  3:  3.7905 -  3.3170 0.99   1312  144 0.1031 0.1504      5.4577       5.853|
|  4:  3.3170 -  3.0163 0.99   1299  153 0.1177 0.1588      5.4504      5.5884|
|  5:  3.0163 -  2.8016 0.99   1296  140 0.1321 0.1850      5.3218      5.5792|
|  6:  2.8016 -  2.6373 0.99   1288  140 0.1188 0.1708      5.2068      5.4245|
|  7:  2.6373 -  2.5058 0.99   1289  138 0.1237 0.1603      5.1673      5.3707|
|  8:  2.5058 -  2.3972 0.98   1256  150 0.1110 0.1812      5.0232      5.3728|
|  9:  2.3972 -  2.3052 0.98   1272  144 0.1130 0.1685      5.0114      5.2991|
| 10:  2.3052 -  2.2259 1.00   1276  139 0.1063 0.1803      4.9326      5.2531|
| 11:  2.2259 -  2.1565 0.98   1273  136 0.1114 0.1765       4.959      5.2764|
| 12:  2.1565 -  2.0951 0.98   1253  140 0.1092 0.1667       4.882      5.1461|
| 13:  2.0951 -  2.0400 1.00   1260  139 0.1131 0.1802      4.7923       5.101|
| 14:  2.0400 -  1.9904 0.64    831   95 0.1019 0.1660       4.656      4.9104|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7512  1390   155  0.94   8.86   0.97     0.95       6949.45|
|  2:  4.7512 -  3.7905  1335   146  0.95   7.95   1.01     1.00       8842.58|
|  3:  3.7905 -  3.3170  1312   144  0.94  11.01   1.02     1.02      10030.05|
|  4:  3.3170 -  3.0163  1299   153  0.92  13.45   1.01     0.98      10290.60|
|  5:  3.0163 -  2.8016  1296   140  0.90  16.25   0.99     0.97       8405.55|
|  6:  2.8016 -  2.6373  1288   140  0.90  15.76   0.99     0.96       7194.93|
|  7:  2.6373 -  2.5058  1289   138  0.91  15.58   1.00     0.97       6342.94|
|  8:  2.5058 -  2.3972  1256   150  0.91  14.88   0.99     0.96       4910.73|
|  9:  2.3972 -  2.3052  1272   144  0.91  14.70   1.00     0.96       4754.29|
| 10:  2.3052 -  2.2259  1276   139  0.91  15.29   1.00     0.97       4252.68|
| 11:  2.2259 -  2.1565  1273   136  0.90  16.34   0.99     0.94       4547.42|
| 12:  2.1565 -  2.0951  1253   140  0.91  15.29   1.01     1.00       4104.19|
| 13:  2.0951 -  2.0400  1260   139  0.90  16.49   1.00     0.98       3444.31|
| 14:  2.0400 -  1.9904   831    95  0.92  14.56   0.97     0.94       2571.97|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2571.97 max =        10290.60 mean =      6317.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.76 mean =        13.96|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.035)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    88.27   17.12    None  None   None       |
|    all(noH): 2823   0      0.46    88.27   17.12    None  None   None       |
|    Sol.    : 438    0      5.20    84.08   39.90    None  None   None       |
|    Mac.    : 2385   0      0.46    88.27   12.94    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:     0.463 -   9.244:  872   |   5:    44.369 -  53.150:   98        |
|      1:     9.244 -  18.026: 1218   |   6:    53.150 -  61.931:   73        |
|      2:    18.026 -  26.807:  260   |   7:    61.931 -  70.712:   30        |
|      3:    26.807 -  35.588:  144   |   8:    70.712 -  79.493:   10        |
|      4:    35.588 -  44.369:  111   |   9:    79.493 -  88.275:    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)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.462 - 4.632
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.714 - 4.632

peak=    5.539 closest distance to " CG  PRO A  54 " =    1.260
peak=    5.488 closest distance to " O   HOH Z 111 " =    2.199
peak=    5.427 closest distance to " CB  GLN A 223 " =    1.457
peak=    5.149 closest distance to " O   HOH Z 232 " =    2.291
peak=    5.148 closest distance to " O   HOH Z 126 " =    1.941
peak=    5.148 closest distance to " NE2 GLN A  11 " =    1.131
peak=    5.055 closest distance to " CB  SER A  63 " =    1.254
peak=    4.978 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.849 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.760 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.704 closest distance to " C   PRO A 198 " =    1.517
peak=    4.687 closest distance to " O   HOH Z 298 " =    1.958
peak=    4.614 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.602 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.537 closest distance to " O   HOH Z 369 " =    2.089
peak=    4.511 closest distance to " O   HOH Z  78 " =    1.683
peak=    4.498 closest distance to " O   HOH Z 144 " =    1.721
peak=    4.452 closest distance to " CA  TYR A  30 " =    0.963
peak=    4.413 closest distance to " CB  GLU A 128 " =    1.055
peak=    4.359 closest distance to " O   HOH Z  15 " =    2.229
peak=    4.345 closest distance to " CB  ASN A 148 " =    1.399
peak=    4.329 closest distance to " O   HOH Z 427 " =    2.980
peak=    4.301 closest distance to " CG  PRO A 198 " =    1.246
peak=    4.299 closest distance to " CB  ARG A  79 " =    1.444
peak=    4.292 closest distance to " O   HOH Z 193 " =    1.824
peak=    4.287 closest distance to " O   HOH Z 236 " =    2.104
peak=    4.271 closest distance to " CB  ASN A 187 " =    1.301
peak=    4.256 closest distance to " CG  PRO A  90 " =    1.021
peak=    4.214 closest distance to " CB  TRP A 266 " =    0.975
peak=    4.204 closest distance to " CB  GLU A 152 " =    1.248
peak=    4.196 closest distance to " OD1 ASN A  69 " =    2.596
peak=    4.125 closest distance to " CB  TYR A 169 " =    0.750
peak=    4.107 closest distance to " ND2 ASN A 187 " =    1.395
peak=    4.093 closest distance to " O   HOH Z 193 " =    1.810
peak=    4.062 closest distance to " CA  MET A  40 " =    1.148
peak=    4.054 closest distance to " CB  ARG A 190 " =    1.625
peak=    4.045 closest distance to " O   HOH Z 368 " =    2.034
peak=    4.023 closest distance to " NH1AARG A 145 " =    1.155
peak=    4.023 closest distance to " O   HOH Z 132 " =    2.483
peak=    4.019 closest distance to " CE  LYS A  76 " =    0.850
peak=    4.004 closest distance to " O   HOH Z 316 " =    3.063
peak=    4.004 closest distance to " O   HOH Z 261 " =    2.080
peak=    3.995 closest distance to " O   HOH Z 234 " =    3.807
peak=    3.980 closest distance to " CB  SER A 212 " =    1.095
peak=    3.980 closest distance to " O   HOH Z 214 " =    2.016
peak=    3.976 closest distance to " O   HOH Z 250 " =    1.467
peak=    3.969 closest distance to " O   HOH Z 303 " =    2.150
peak=    3.951 closest distance to " OD2 ASP A 286 " =    2.887
peak=    3.947 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.946 closest distance to " CA  ASN A 215 " =    1.243
peak=    3.936 closest distance to " CZ  PHE A 218 " =    1.064
peak=    3.918 closest distance to " ND1 HIS A  86 " =    1.722
peak=    3.913 closest distance to " CD  ARG A  66 " =    2.193
peak=    3.909 closest distance to " O   HOH Z 180 " =    2.124
peak=    3.907 closest distance to " O   HOH Z 189 " =    2.486
peak=    3.896 closest distance to " O   HOH Z  61 " =    1.618
peak=    3.895 closest distance to " CG2 VAL A 257 " =    0.969
peak=    3.895 closest distance to " O   HOH Z 346 " =    1.627
peak=    3.882 closest distance to " CD BLYS A 290 " =    1.018
peak=    3.880 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.874 closest distance to " CG2 THR A 221 " =    1.022
peak=    3.857 closest distance to " O   HOH Z   1 " =    1.956
peak=    3.850 closest distance to " O   HOH Z 158 " =    2.893
peak=    3.850 closest distance to " CB  VAL A 265 " =    1.258
peak=    3.840 closest distance to " O   HOH Z  54 " =    2.356
peak=    3.839 closest distance to " O   HOH Z 411 " =    3.846
peak=    3.834 closest distance to " O   HOH Z 108 " =    2.341
peak=    3.828 closest distance to " O   HOH Z 135 " =    1.743
peak=    3.823 closest distance to " CG1 ILE A  33 " =    1.215
peak=    3.814 closest distance to " O   HOH Z 389 " =    1.936
peak=    3.807 closest distance to " O   HOH Z 217 " =    3.109
peak=    3.797 closest distance to " CB  VAL A 202 " =    1.650
peak=    3.789 closest distance to " O   MET A 105 " =    1.841
peak=    3.788 closest distance to " O   HOH Z 203 " =    1.876
peak=    3.783 closest distance to " O   HOH Z 133 " =    2.488
peak=    3.783 closest distance to " O   HOH Z 213 " =    1.955
peak=    3.778 closest distance to " CB  ASP A 140 " =    0.932
peak=    3.769 closest distance to " CG  PRO A 243 " =    1.055
peak=    3.758 closest distance to " CB  SER A 216 " =    0.870
peak=    3.755 closest distance to " CA  THR A 264 " =    0.854
peak=    3.754 closest distance to " O   HOH Z   9 " =    2.082
peak=    3.747 closest distance to " CB  SER A   3 " =    1.397
peak=    3.746 closest distance to " NH2 ARG A 156 " =    1.216
peak=    3.728 closest distance to " O   HOH Z 386 " =    3.137
peak=    3.721 closest distance to " O   HOH Z 272 " =    1.874
peak=    3.717 closest distance to " CA  ALA A  21 " =    1.192
peak=    3.703 closest distance to " CB  GLU A 277 " =    3.671
peak=    3.692 closest distance to " O   HOH Z 219 " =    2.061
peak=    3.690 closest distance to " O   HOH Z  10 " =    1.859
peak=    3.684 closest distance to " O   HOH Z 133 " =    1.721
peak=    3.680 closest distance to " CA  TYR A  30 " =    1.052
peak=    3.670 closest distance to " O   HOH Z 425 " =    1.232
peak=    3.647 closest distance to " O   HOH Z 344 " =    3.215
peak=    3.625 closest distance to " O   HOH Z  20 " =    1.678
peak=    3.622 closest distance to " O   HOH Z  88 " =    3.562
peak=    3.614 closest distance to " CB  ALA A  34 " =    1.118
peak=    3.612 closest distance to " N   ASN A 127 " =    1.262
peak=    3.612 closest distance to " O   HOH Z 280 " =    3.033
peak=    3.609 closest distance to " O   HOH Z  21 " =    1.715
peak=    3.606 closest distance to " CA  ARG A 195 " =    1.283
peak=    3.604 closest distance to " NH2BARG A 145 " =    2.087
peak=    3.603 closest distance to " O   THR A 251 " =    1.232
peak=    3.597 closest distance to " CB  MET A  47 " =    1.037
peak=    3.595 closest distance to " O   HOH Z 437 " =    1.390
peak=    3.593 closest distance to " CA  THR A 221 " =    1.010
peak=    3.592 closest distance to " CD  ARG A 219 " =    1.098
peak=    3.583 closest distance to " O   HOH Z 305 " =    3.623
peak=    3.583 closest distance to " CD2 LEU A 255 " =    1.490
peak=    3.581 closest distance to " CB  TRP A 179 " =    1.484
peak=    3.570 closest distance to " CB  TYR A 116 " =    0.834
peak=    3.568 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.540 closest distance to " N   ARG A 156 " =    1.314
peak=    3.538 closest distance to " O   HOH Z 425 " =    2.131
peak=    3.536 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.533 closest distance to " CB  MET A  40 " =    0.804
peak=    3.528 closest distance to " CB  ASN A  39 " =    0.917
peak=    3.520 closest distance to " O   SER A  87 " =    2.333
peak=    3.520 closest distance to " O   HOH Z 172 " =    3.385
peak=    3.509 closest distance to " OG  SER A  22 " =    2.818
peak=    3.501 closest distance to " O   HOH Z  40 " =    2.069
peak=    3.501 closest distance to " CA  ALA A 158 " =    1.185
peak=    3.493 closest distance to " CB  ASN A 142 " =    1.006
peak=    3.492 closest distance to " CD2 TRP A 179 " =    1.358
peak=    3.481 closest distance to " O   HOH Z 403 " =    1.699
peak=    3.480 closest distance to " O   HOH Z 371 " =    3.092
peak=    3.468 closest distance to " CB  LEU A 143 " =    1.107
peak=    3.466 closest distance to " O   THR A 220 " =    1.318
peak=    3.463 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.460 closest distance to " CD  LYS A 166 " =    1.258
peak=    3.459 closest distance to " CA  ALA A 291 " =    0.910
peak=    3.453 closest distance to " CD  ARG A 269 " =    0.932
peak=    3.450 closest distance to " O   HOH Z 285 " =    2.936
peak=    3.449 closest distance to " CA  ALA A  51 " =    0.947
peak=    3.445 closest distance to " O   HOH Z 193 " =    2.122
peak=    3.439 closest distance to " O   HOH Z   1 " =    1.758
peak=    3.439 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.424 closest distance to " O   HOH Z  64 " =    2.104
peak=    3.422 closest distance to " O   HOH Z 147 " =    1.760
peak=    3.416 closest distance to " O   HOH Z  40 " =    1.852
peak=    3.415 closest distance to " O   HOH Z 426 " =    1.607
peak=    3.414 closest distance to " O   HOH Z 391 " =    2.956
peak=    3.411 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.402 closest distance to " O   HOH Z  68 " =    2.160
peak=    3.401 closest distance to " O   HOH Z 271 " =    2.414
peak=    3.394 closest distance to " OD1 ASN A 217 " =    1.656
peak=    3.390 closest distance to " O   HOH Z 329 " =    3.794
peak=    3.390 closest distance to " CB  THR A 157 " =    1.142
peak=    3.386 closest distance to " N   PHE A 130 " =    1.281
peak=    3.384 closest distance to " CB  ALA A   1 " =    4.632
peak=    3.384 closest distance to " CB  ALA A 291 " =    1.419
peak=    3.381 closest distance to " CG1 VAL A 153 " =    0.981
peak=    3.381 closest distance to " O   HOH Z 371 " =    1.734
peak=    3.373 closest distance to " CD1 LEU A 228 " =    2.069
peak=    3.372 closest distance to " NE2 HIS A 207 " =    1.398
peak=    3.370 closest distance to " O   HOH Z  61 " =    1.485
peak=    3.368 closest distance to " O   HOH Z 209 " =    2.379
peak=    3.367 closest distance to " ND1 HIS A  81 " =    1.574
peak=    3.367 closest distance to " O   HOH Z 359 " =    3.899
peak=    3.365 closest distance to " O   HOH Z  59 " =    1.954
peak=    3.364 closest distance to " CG1BVAL A  72 " =    1.630
peak=    3.357 closest distance to " O   ALA A 165 " =    1.439
peak=    3.356 closest distance to " O  BHOH Z 338 " =    2.341
peak=    3.353 closest distance to " CD1 ILE A 106 " =    0.746
peak=    3.353 closest distance to " N   ASN A  39 " =    1.340
peak=    3.351 closest distance to " OD1BASN A 224 " =    2.342
peak=    3.349 closest distance to " CZ  PHE A 192 " =    0.893
peak=    3.349 closest distance to " O   HOH Z  44 " =    3.092
peak=    3.347 closest distance to " CB  GLU A 236 " =    1.229
peak=    3.345 closest distance to " O   HOH Z 273 " =    2.775
peak=    3.334 closest distance to " O   HOH Z 188 " =    2.158
peak=    3.334 closest distance to " CB  ASN A 110 " =    1.223
peak=    3.334 closest distance to " CA  ASP A 191 " =    0.798
peak=    3.332 closest distance to " O   ALA A 158 " =    1.324
peak=    3.330 closest distance to " O   HOH Z 134 " =    1.322
peak=    3.328 closest distance to " CB  ALA A 248 " =    0.973
peak=    3.328 closest distance to " CB  THR A  82 " =    1.393
peak=    3.327 closest distance to " CD  LYS A 119 " =    1.243
peak=    3.321 closest distance to " ND2 ASN A 110 " =    1.785
peak=    3.319 closest distance to " O   HOH Z 211 " =    2.822
peak=    3.317 closest distance to " O   HOH Z 166 " =    3.719
peak=    3.315 closest distance to " N   VAL A 126 " =    1.229
peak=    3.314 closest distance to " O   HOH Z 128 " =    2.267
peak=    3.308 closest distance to " CG  GLN A  88 " =    1.040
peak=    3.307 closest distance to " NH2AARG A 190 " =    1.956
peak=    3.304 closest distance to " O   TYR A 116 " =    1.304
peak=    3.302 closest distance to " O   HOH Z 286 " =    2.269
peak=    3.302 closest distance to " O   HOH Z 409 " =    2.794
peak=    3.298 closest distance to " CB  ILE A 120 " =    1.248
peak=    3.290 closest distance to " CB  LEU A 255 " =    0.822
peak=    3.290 closest distance to " CB  ALA A 233 " =    1.353
peak=    3.290 closest distance to " OG BSER A 164 " =    2.317
peak=    3.289 closest distance to " CG1 ILE A 151 " =    0.984
peak=    3.288 closest distance to " CB  GLU A  46 " =    1.017
peak=    3.288 closest distance to " CA  LYS A 290 " =    1.322
peak=    3.287 closest distance to " CA  SER A  87 " =    1.049
peak=    3.285 closest distance to " CA  GLY A 267 " =    1.227
peak=    3.280 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.279 closest distance to " CA  LYS A 117 " =    1.192
peak=    3.278 closest distance to " CD  ARG A  14 " =    1.287
peak=    3.278 closest distance to " CG  LYS A  76 " =    0.975
peak=    3.274 closest distance to " N   SER A 146 " =    1.727
peak=    3.274 closest distance to " O   HOH Z  53 " =    2.553
peak=    3.271 closest distance to " O   HOH Z 423 " =    1.491
peak=    3.270 closest distance to " CA  ARG A  36 " =    1.167
peak=    3.267 closest distance to " O   HOH Z 407 " =    2.371
peak=    3.266 closest distance to " O   HOH Z 327 " =    2.022
peak=    3.264 closest distance to " O   HOH Z   1 " =    2.273
peak=    3.259 closest distance to " O   HOH Z 185 " =    1.813
peak=    3.258 closest distance to " CB  ALA A   9 " =    1.557
peak=    3.253 closest distance to " O   HOH Z 183 " =    1.404
peak=    3.252 closest distance to " CB  ALA A 104 " =    0.726
peak=    3.244 closest distance to " O   HOH Z  88 " =    2.895
peak=    3.241 closest distance to " O   HOH Z 109 " =    2.646
peak=    3.238 closest distance to " N   SER A 134 " =    1.330
peak=    3.237 closest distance to " O   HOH Z 402 " =    1.452
peak=    3.235 closest distance to " O   HOH Z 411 " =    1.852
peak=    3.234 closest distance to " CB  HIS A 108 " =    0.818
peak=    3.234 closest distance to " CA  ALA A 233 " =    1.196
peak=    3.230 closest distance to " O   HOH Z 291 " =    1.719
peak=    3.223 closest distance to " CA  MET A 105 " =    1.021
peak=    3.221 closest distance to " CA  ILE A 234 " =    1.004
peak=    3.215 closest distance to " CB  PHE A  16 " =    0.994
peak=    3.213 closest distance to " O   HOH Z 345 " =    3.575
peak=    3.213 closest distance to " CA  GLU A  46 " =    0.714
peak=    3.211 closest distance to " CD2 LEU A 297 " =    0.868
peak=    3.210 closest distance to " O   GLY A  57 " =    2.629
peak=    3.210 closest distance to " O   HOH Z 295 " =    1.491
peak=    3.208 closest distance to " CB  LYS A 117 " =    1.181
peak=    3.208 closest distance to " CB  LEU A 237 " =    0.751
peak=    3.207 closest distance to " N   TYR A  15 " =    0.759
peak=    3.206 closest distance to " CA  ALA A 160 " =    0.905
peak=    3.206 closest distance to " CZ  ARG A  14 " =    2.024
peak=    3.206 closest distance to " CG  MET A 113 " =    1.475
peak=    3.204 closest distance to " NH2 ARG A 219 " =    1.796
peak=    3.203 closest distance to " CG BARG A 275 " =    1.519
peak=    3.202 closest distance to " N   GLN A 278 " =    1.066
peak=    3.201 closest distance to " O   HOH Z 148 " =    3.347
peak=    3.196 closest distance to " O   HOH Z 245 " =    1.235
peak=    3.196 closest distance to " CG  ARG A 159 " =    0.885
peak=    3.193 closest distance to " CA  ASP A 140 " =    1.178
peak=    3.190 closest distance to " CD  GLN A 240 " =    1.652
peak=    3.182 closest distance to " O   HOH Z  97 " =    1.958
peak=    3.179 closest distance to " O   HOH Z  93 " =    2.827
peak=    3.179 closest distance to " O   ALA A 291 " =    1.480
peak=    3.175 closest distance to " CB  TRP A 150 " =    1.332
peak=    3.175 closest distance to " O   HOH Z  58 " =    1.483
peak=    3.174 closest distance to " CG  GLN A  11 " =    1.740
peak=    3.174 closest distance to " CB  TYR A  30 " =    1.448
peak=    3.173 closest distance to " CB  SER A 276 " =    1.112
peak=    3.173 closest distance to " O   HOH Z 423 " =    2.796
peak=    3.172 closest distance to " CD2 HIS A  81 " =    1.088
peak=    3.165 closest distance to " CB  ARG A 138 " =    1.008
peak=    3.165 closest distance to " O   HOH Z 365 " =    2.955
peak=    3.165 closest distance to " CB  ASN A 224 " =    1.016
peak=    3.162 closest distance to " O   HOH Z 116 " =    1.749
peak=    3.161 closest distance to " O   HOH Z 353 " =    2.765
peak=    3.161 closest distance to " OG  SER A  62 " =    3.075
peak=    3.157 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.156 closest distance to " CB  PRO A 163 " =    4.169
peak=    3.151 closest distance to " CG  GLN A 278 " =    1.347
peak=    3.149 closest distance to " NH2AARG A 275 " =    3.683
peak=    3.146 closest distance to " CG2 VAL A 174 " =    1.357
peak=    3.146 closest distance to " CB  ASP A 171 " =    0.871
peak=    3.146 closest distance to " CA  ASN A 217 " =    1.191
peak=    3.138 closest distance to " CA  LEU A 101 " =    1.480
peak=    3.134 closest distance to " OG  SER A 206 " =    1.264
peak=    3.132 closest distance to " CA  ARG A 102 " =    1.176
peak=    3.130 closest distance to " CD  PRO A 243 " =    1.669
peak=    3.127 closest distance to " CB  LYS A 193 " =    1.013
peak=    3.125 closest distance to " O   HOH Z 144 " =    1.766
peak=    3.124 closest distance to " O   HOH Z 406 " =    1.601
peak=    3.123 closest distance to " O   HOH Z 299 " =    2.476
peak=    3.123 closest distance to " CG2 ILE A 120 " =    1.070
peak=    3.121 closest distance to " CB  TYR A 169 " =    1.264
peak=    3.118 closest distance to " O   HOH Z 379 " =    3.422
peak=    3.118 closest distance to " O   HOH Z 175 " =    2.124
peak=    3.110 closest distance to " CB  GLU A 152 " =    1.453
peak=    3.110 closest distance to " O   HOH Z 373 " =    1.540
peak=    3.107 closest distance to " O   HOH Z 128 " =    2.194
peak=    3.105 closest distance to " OG  SER A  62 " =    3.068
peak=    3.104 closest distance to " O   HOH Z 386 " =    2.921
peak=    3.096 closest distance to " N   SER A 135 " =    1.299
peak=    3.085 closest distance to " CA  TYR A 186 " =    1.578
peak=    3.084 closest distance to " CB  PHE A 283 " =    0.870
peak=    3.081 closest distance to " O   HOH Z  49 " =    2.171
peak=    3.075 closest distance to " CD2 LEU A 255 " =    1.125
peak=    3.072 closest distance to " CB  ASN A 285 " =    0.813
peak=    3.064 closest distance to " CB  ILE A 234 " =    1.157
peak=    3.056 closest distance to " O   HOH Z 302 " =    1.832
peak=    3.052 closest distance to " O   HOH Z 213 " =    2.073
peak=    3.041 closest distance to " O   HOH Z 213 " =    2.924
peak=    3.013 closest distance to " CB  TRP A 179 " =    1.716
peak=    3.003 closest distance to " CA  ARG A  56 " =    2.071

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.723 - 5.619
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.723 - 5.619

peak=   -4.572 closest distance to " CB  PRO A 243 " =    2.592
peak=   -4.560 closest distance to " O   HOH Z 266 " =    4.992
peak=   -4.427 closest distance to " O   HOH Z 377 " =    1.987
peak=   -4.419 closest distance to " CD  ARG A 156 " =    2.015
peak=   -4.368 closest distance to " CG  GLN A 223 " =    2.010
peak=   -4.338 closest distance to " O   HOH Z 198 " =    2.109
peak=   -4.213 closest distance to " CD  ARG A  14 " =    3.495
peak=   -4.152 closest distance to " O   VAL A  67 " =    2.785
peak=   -4.098 closest distance to " O   HOH Z 389 " =    1.934
peak=   -4.095 closest distance to " O   HOH Z 231 " =    2.127
peak=   -4.093 closest distance to " CE2 TYR A  30 " =    2.803
peak=   -4.042 closest distance to " C   ASN A 187 " =    1.865
peak=   -4.026 closest distance to " CG1 VAL A 112 " =    2.905
peak=   -4.008 closest distance to " N   ALA A  43 " =    2.745
peak=   -4.004 closest distance to " O   HOH Z  43 " =    1.518
peak=   -3.990 closest distance to " O   HOH Z  38 " =    1.387
peak=   -3.954 closest distance to " O   HOH Z 372 " =    2.447
peak=   -3.934 closest distance to " O   HOH Z 353 " =    2.100
peak=   -3.926 closest distance to " CZ3 TRP A 179 " =    1.068
peak=   -3.890 closest distance to " O   HOH Z 435 " =    2.792
peak=   -3.889 closest distance to " OG BSER A 134 " =    1.221
peak=   -3.884 closest distance to " C   ASN A 285 " =    2.508
peak=   -3.869 closest distance to " O   HOH Z  52 " =    1.285
peak=   -3.863 closest distance to " ND2 ASN A  45 " =    1.437
peak=   -3.842 closest distance to " O   ILE A 109 " =    2.675
peak=   -3.830 closest distance to " CD1 PHE A  59 " =    1.848
peak=   -3.817 closest distance to " O   HOH Z 290 " =    1.271
peak=   -3.808 closest distance to " CG  ARG A 269 " =    2.598
peak=   -3.806 closest distance to " CZ  PHE A  59 " =    1.587
peak=   -3.804 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.802 closest distance to " CB  ALA A  43 " =    2.566
peak=   -3.800 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.795 closest distance to " CA  GLY A 203 " =    2.309
peak=   -3.785 closest distance to " ND2 ASN A  45 " =    1.109
peak=   -3.783 closest distance to " O   HOH Z  60 " =    2.525
peak=   -3.781 closest distance to " OD1 ASN A 187 " =    1.625
peak=   -3.780 closest distance to " O   HOH Z 118 " =    3.090
peak=   -3.773 closest distance to " NH2AARG A 275 " =    5.551
peak=   -3.754 closest distance to " O   HOH Z 407 " =    3.304
peak=   -3.741 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.738 closest distance to " C   HIS A 108 " =    1.083
peak=   -3.730 closest distance to " CB  PHE A 192 " =    1.964
peak=   -3.729 closest distance to " O   GLY A 211 " =    1.469
peak=   -3.712 closest distance to " CD2 LEU A 237 " =    2.823
peak=   -3.684 closest distance to " CE  MET A 105 " =    2.254
peak=   -3.680 closest distance to " O   HOH Z  73 " =    2.052
peak=   -3.675 closest distance to " CB  PRO A  54 " =    2.498
peak=   -3.671 closest distance to " CB  PHE A 283 " =    2.868
peak=   -3.667 closest distance to " CG  MET A 105 " =    0.982
peak=   -3.658 closest distance to " O   HOH Z 313 " =    1.896
peak=   -3.651 closest distance to " CZ BARG A 275 " =    1.817
peak=   -3.643 closest distance to " NE2 GLN A  88 " =    2.005
peak=   -3.637 closest distance to " CG1 VAL A 250 " =    2.614
peak=   -3.631 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.614 closest distance to " CB  ASN A  39 " =    2.313
peak=   -3.613 closest distance to " O   VAL A 189 " =    2.534
peak=   -3.608 closest distance to " OD1 ASN A 148 " =    1.579
peak=   -3.606 closest distance to " CD1 LEU A 228 " =    2.356
peak=   -3.600 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.599 closest distance to " CD1 LEU A 101 " =    2.348
peak=   -3.593 closest distance to " OD1 ASP A 191 " =    1.788
peak=   -3.577 closest distance to " C   ALA A 158 " =    1.344
peak=   -3.565 closest distance to " ND2 ASN A 249 " =    2.284
peak=   -3.564 closest distance to " OD2 ASP A 171 " =    1.832
peak=   -3.563 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.554 closest distance to " CD  GLN A  58 " =    1.034
peak=   -3.551 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.536 closest distance to " CA  GLY A 241 " =    2.276
peak=   -3.535 closest distance to " CG2 ILE A 263 " =    2.359
peak=   -3.534 closest distance to " CB  ALA A 291 " =    2.351
peak=   -3.524 closest distance to " O   HOH Z 211 " =    1.599
peak=   -3.523 closest distance to " CB  ASP A  27 " =    2.502
peak=   -3.520 closest distance to " NH1 ARG A 195 " =    2.617
peak=   -3.511 closest distance to " O   PRO A 163 " =    2.029
peak=   -3.508 closest distance to " N   THR A 157 " =    1.536
peak=   -3.492 closest distance to " OG  SER A  87 " =    1.417
peak=   -3.485 closest distance to " C   LEU A 222 " =    0.723
peak=   -3.474 closest distance to " OXT GLY A 302 " =    2.949
peak=   -3.469 closest distance to " CD  ARG A 195 " =    5.161
peak=   -3.464 closest distance to " CE2 PHE A 218 " =    2.465
peak=   -3.462 closest distance to " O   HOH Z 185 " =    2.272
peak=   -3.459 closest distance to " N   SER A 212 " =    1.958
peak=   -3.452 closest distance to " OD1 ASP A 171 " =    1.568
peak=   -3.451 closest distance to " CE2 PHE A  61 " =    2.609
peak=   -3.446 closest distance to " O   HOH Z 350 " =    1.640
peak=   -3.435 closest distance to " O   ALA A 180 " =    1.350
peak=   -3.435 closest distance to " C   LEU A 143 " =    1.321
peak=   -3.429 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.426 closest distance to " O   HOH Z 298 " =    2.519
peak=   -3.422 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.420 closest distance to " O   HOH Z 426 " =    1.646
peak=   -3.419 closest distance to " O   HOH Z  11 " =    1.860
peak=   -3.417 closest distance to " CD  ARG A 139 " =    1.559
peak=   -3.408 closest distance to " O   HOH Z  51 " =    1.724
peak=   -3.401 closest distance to " OD1 ASP A 191 " =    1.576
peak=   -3.400 closest distance to " O   HOH Z 207 " =    2.207
peak=   -3.390 closest distance to " CG1 VAL A 197 " =    2.260
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.692
peak=   -3.381 closest distance to " CB  CYS A 254 " =    2.198
peak=   -3.378 closest distance to " O   HOH Z 253 " =    4.061
peak=   -3.378 closest distance to " OG  SER A  97 " =    2.170
peak=   -3.375 closest distance to " CA  GLY A 241 " =    3.047
peak=   -3.374 closest distance to " O   HOH Z 198 " =    1.497
peak=   -3.373 closest distance to " O   HOH Z 102 " =    1.632
peak=   -3.368 closest distance to " O   HOH Z  13 " =    1.627
peak=   -3.363 closest distance to " CG  TRP A 266 " =    1.729
peak=   -3.362 closest distance to " CD2 TYR A 293 " =    2.054
peak=   -3.359 closest distance to " N   GLN A  58 " =    1.761
peak=   -3.356 closest distance to " O   PRO A 198 " =    1.338
peak=   -3.350 closest distance to " CE BMET A  47 " =    1.897
peak=   -3.347 closest distance to " CD  LYS A 289 " =    2.446
peak=   -3.346 closest distance to " ND2 ASN A  60 " =    1.485
peak=   -3.345 closest distance to " CB  TYR A  15 " =    2.148
peak=   -3.342 closest distance to " CA  GLY A  98 " =    1.966
peak=   -3.340 closest distance to " O   HOH Z 275 " =    1.501
peak=   -3.336 closest distance to " CG  GLN A  88 " =    0.875
peak=   -3.335 closest distance to " O   HOH Z 292 " =    4.627
peak=   -3.335 closest distance to " O   HOH Z 394 " =    1.433
peak=   -3.333 closest distance to " CB  ALA A   9 " =    2.593
peak=   -3.325 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.323 closest distance to " CB  ALA A 131 " =    2.052
peak=   -3.310 closest distance to " O   HOH Z  98 " =    2.156
peak=   -3.307 closest distance to " SG ACYS A 201 " =    1.931
peak=   -3.302 closest distance to " O   HOH Z 111 " =    2.102
peak=   -3.294 closest distance to " O   SER A 135 " =    1.449
peak=   -3.293 closest distance to " CG  PRO A 163 " =    2.399
peak=   -3.289 closest distance to " O   HOH Z 311 " =    3.744
peak=   -3.288 closest distance to " NH1AARG A 275 " =    1.802
peak=   -3.287 closest distance to " O   VAL A 153 " =    2.258
peak=   -3.285 closest distance to " CB  TRP A  85 " =    2.396
peak=   -3.284 closest distance to " O   VAL A  67 " =    2.632
peak=   -3.283 closest distance to " O   HOH Z   6 " =    1.598
peak=   -3.283 closest distance to " O   SER A  62 " =    2.221
peak=   -3.275 closest distance to " O   HOH Z 196 " =    2.169
peak=   -3.274 closest distance to " O   GLY A 203 " =    2.429
peak=   -3.269 closest distance to " O   HOH Z 281 " =    2.649
peak=   -3.266 closest distance to " O   HOH Z 350 " =    2.558
peak=   -3.261 closest distance to " CB  ASP A 132 " =    2.328
peak=   -3.261 closest distance to " CB  CYS A 201 " =    2.499
peak=   -3.260 closest distance to " O   HOH Z 184 " =    1.844
peak=   -3.259 closest distance to " CB  ALA A 248 " =    1.985
peak=   -3.257 closest distance to " N   ALA A 226 " =    2.219
peak=   -3.250 closest distance to " N   THR A 235 " =    1.339
peak=   -3.246 closest distance to " O   PRO A 243 " =    2.535
peak=   -3.242 closest distance to " O   TRP A  70 " =    1.511
peak=   -3.241 closest distance to " O   HOH Z 292 " =    1.700
peak=   -3.240 closest distance to " OG  SER A  62 " =    1.670
peak=   -3.238 closest distance to " N   LYS A 166 " =    2.008
peak=   -3.232 closest distance to " CD2 PHE A 225 " =    1.161
peak=   -3.229 closest distance to " CG2 VAL A 189 " =    1.998
peak=   -3.226 closest distance to " O   HOH Z 393 " =    1.391
peak=   -3.226 closest distance to " NE  ARG A  36 " =    1.962
peak=   -3.221 closest distance to " CB  ASP A 286 " =    2.144
peak=   -3.219 closest distance to " O   ALA A 161 " =    1.645
peak=   -3.218 closest distance to " CD2 PHE A  61 " =    1.993
peak=   -3.217 closest distance to " OH  TYR A 214 " =    1.246
peak=   -3.202 closest distance to " CD1 LEU A 297 " =    2.505
peak=   -3.200 closest distance to " CA  SER A 135 " =    1.332
peak=   -3.197 closest distance to " O   GLY A 196 " =    1.148
peak=   -3.197 closest distance to " OE1 GLN A  88 " =    1.190
peak=   -3.196 closest distance to " O   HOH Z 298 " =    1.221
peak=   -3.192 closest distance to " O   HOH Z 324 " =    2.305
peak=   -3.187 closest distance to " OH  TYR A 169 " =    1.064
peak=   -3.186 closest distance to " O   HOH Z 191 " =    5.619
peak=   -3.185 closest distance to " O   HOH Z 103 " =    1.891
peak=   -3.182 closest distance to " O   HOH Z 417 " =    2.562
peak=   -3.180 closest distance to " CG1 VAL A 112 " =    2.601
peak=   -3.179 closest distance to " O   VAL A 125 " =    2.342
peak=   -3.177 closest distance to " NH2 ARG A  79 " =    1.913
peak=   -3.171 closest distance to " CD1 LEU A 228 " =    2.284
peak=   -3.170 closest distance to " O   HOH Z  90 " =    1.602
peak=   -3.162 closest distance to " CB  ALA A 248 " =    2.452
peak=   -3.160 closest distance to " CE1 TYR A 169 " =    2.505
peak=   -3.159 closest distance to " N   SER A 276 " =    1.263
peak=   -3.155 closest distance to " O   HOH Z 417 " =    2.699
peak=   -3.154 closest distance to " CB  PHE A  16 " =    2.549
peak=   -3.150 closest distance to " O   HOH Z 252 " =    4.241
peak=   -3.147 closest distance to " O   ALA A  10 " =    1.685
peak=   -3.139 closest distance to " O   HOH Z 295 " =    1.528
peak=   -3.135 closest distance to " O   HOH Z 359 " =    3.181
peak=   -3.131 closest distance to " C   MET A 188 " =    1.437
peak=   -3.131 closest distance to " NH2 ARG A 159 " =    2.453
peak=   -3.129 closest distance to " OD1 ASN A 301 " =    1.942
peak=   -3.129 closest distance to " O   HOH Z  22 " =    2.642
peak=   -3.126 closest distance to " O   HOH Z  44 " =    2.209
peak=   -3.124 closest distance to " CB  ASP A 132 " =    2.265
peak=   -3.120 closest distance to " CG2 ILE A  20 " =    2.780
peak=   -3.106 closest distance to " O   VAL A 197 " =    1.482
peak=   -3.104 closest distance to " CE  LYS A  76 " =    2.656
peak=   -3.101 closest distance to " O   HOH Z 310 " =    1.790
peak=   -3.098 closest distance to " O   HOH Z 166 " =    1.949
peak=   -3.090 closest distance to " N   ALA A 248 " =    1.574
peak=   -3.089 closest distance to " OE1 GLN A 223 " =    2.121
peak=   -3.078 closest distance to " C   ALA A   8 " =    1.618
peak=   -3.073 closest distance to " O   LEU A 101 " =    2.558
peak=   -3.072 closest distance to " CG2 THR A 221 " =    2.140
peak=   -3.070 closest distance to " C   GLY A  17 " =    1.233
peak=   -3.069 closest distance to " SD  MET A 188 " =    2.254
peak=   -3.065 closest distance to " CG  HIS A  86 " =    0.947
peak=   -3.065 closest distance to " O   GLY A  80 " =    2.412
peak=   -3.062 closest distance to " NH2 ARG A  79 " =    1.550
peak=   -3.053 closest distance to " OXT GLY A 302 " =    3.341
peak=   -3.050 closest distance to " O   HOH Z 263 " =    5.212
peak=   -3.039 closest distance to " O   HOH Z 139 " =    2.967

================= 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    :  0.3291 0.3283   6.054596e+00   6.057439e+00
   1_bss:  0.3154 0.3143   6.032737e+00   6.031295e+00
   1_xyz:  0.1846 0.2068   5.545413e+00   5.649630e+00
   1_adp:  0.1719 0.2109   5.498029e+00   5.668808e+00
   1_occ:  0.1715 0.2105   5.495435e+00   5.667256e+00
   2_bss:  0.1692 0.2085   5.487355e+00   5.659236e+00
   2_xyz:  0.1294 0.1705   5.249334e+00   5.463557e+00
   2_adp:  0.1216 0.1645   5.199669e+00   5.430049e+00
   2_occ:  0.1215 0.1643   5.199415e+00   5.430150e+00
   3_bss:  0.1215 0.1632   5.197557e+00   5.426539e+00
   3_xyz:  0.1133 0.1581   5.150388e+00   5.393450e+00
   3_adp:  0.1127 0.1566   5.145063e+00   5.386974e+00
   3_occ:  0.1127 0.1566   5.145003e+00   5.387240e+00
   4_bss:  0.1126 0.1566   5.144751e+00   5.386857e+00
   4_xyz:  0.1143 0.1575   5.156184e+00   5.394338e+00
   4_adp:  0.1134 0.1581   5.154126e+00   5.397977e+00
   4_occ:  0.1133 0.1581   5.154086e+00   5.398046e+00
   5_bss:  0.1133 0.1581   5.154154e+00   5.398044e+00
   5_xyz:  0.1098 0.1575   5.136405e+00   5.391992e+00
   5_adp:  0.1091 0.1582   5.135003e+00   5.393808e+00
   5_occ:  0.1091 0.1582   5.134944e+00   5.393842e+00
   5_bss:  0.1090 0.1582   5.134850e+00   5.393955e+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:  0.327  50.000   1.886  -2.474  -1.632  -0.000  -0.000  -0.000
   1_xyz:  0.327  50.000   1.886  -2.474  -1.632  -0.000  -0.000  -0.000
   1_adp:  0.327  50.000   1.886  -2.474  -1.632  -0.000  -0.000  -0.000
   1_occ:  0.327  50.000   1.886  -2.474  -1.632  -0.000  -0.000  -0.000
   2_bss:  0.337  58.520  -1.323  -3.029  -1.971  -0.000  -0.000  -0.000
   2_xyz:  0.337  58.520  -1.323  -3.029  -1.971  -0.000  -0.000  -0.000
   2_adp:  0.337  58.520  -1.323  -3.029  -1.971  -0.000  -0.000  -0.000
   2_occ:  0.337  58.520  -1.323  -3.029  -1.971  -0.000  -0.000  -0.000
   3_bss:  0.333  58.520  -2.029  -2.896  -1.809  -0.000  -0.000  -0.000
   3_xyz:  0.333  58.520  -2.029  -2.896  -1.809  -0.000  -0.000  -0.000
   3_adp:  0.333  58.520  -2.029  -2.896  -1.809  -0.000  -0.000  -0.000
   3_occ:  0.333  58.520  -2.029  -2.896  -1.809  -0.000  -0.000  -0.000
   4_bss:  0.333  58.520  -2.232  -2.798  -1.738  -0.000  -0.000  -0.000
   4_xyz:  0.333  58.520  -2.232  -2.798  -1.738  -0.000  -0.000  -0.000
   4_adp:  0.333  58.520  -2.232  -2.798  -1.738  -0.000  -0.000  -0.000
   4_occ:  0.333  58.520  -2.232  -2.798  -1.738  -0.000  -0.000  -0.000
   5_bss:  0.333  58.520  -2.174  -2.660  -1.593  -0.000  -0.000  -0.000
   5_xyz:  0.333  58.520  -2.174  -2.660  -1.593  -0.000  -0.000  -0.000
   5_adp:  0.333  58.520  -2.174  -2.660  -1.593  -0.000  -0.000  -0.000
   5_occ:  0.333  58.520  -2.174  -2.660  -1.593  -0.000  -0.000  -0.000
   5_bss:  0.322  55.306  -1.941  -2.415  -1.364  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.402 0.7116  0.8875    31817.604
   1_bss:  33.212 0.7236  0.8807    28882.538
   1_xyz:  19.664 0.8664  0.9987    11173.216
   1_adp:  20.255 0.8603  0.9967    11640.631
   1_occ:  20.215 0.8605  0.9966    11563.508
   2_bss:  19.947 0.8632  0.9520    11351.742
   2_xyz:  15.438 0.9031  0.9764     7386.682
   2_adp:  14.643 0.9099  0.9794     6857.145
   2_occ:  14.637 0.9099  0.9791     6853.583
   3_bss:  14.562 0.9105  0.9743     6780.963
   3_xyz:  13.916 0.9158  0.9749     6338.012
   3_adp:  13.757 0.9172  0.9728     6270.254
   3_occ:  13.763 0.9172  0.9726     6268.633
   4_bss:  13.756 0.9172  0.9723     6261.596
   4_xyz:  13.866 0.9164  0.9714     6346.707
   4_adp:  13.936 0.9159  0.9671     6379.741
   4_occ:  13.937 0.9159  0.9670     6379.019
   5_bss:  13.938 0.9159  0.9710     6378.852
   5_xyz:  13.848 0.9165  0.9713     6312.699
   5_adp:  13.912 0.9160  0.9654     6321.097
   5_occ:  13.912 0.9160  0.9654     6320.872
   5_bss:  13.912 0.9160  0.9728     6317.492
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6164e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6164e-01
   1_xyz:   1.095  0.008  0.075 14.916  0.005  4.115   6.7107e-02
   1_adp:   1.095  0.008  0.075 14.916  0.005  4.115   6.7107e-02
   1_occ:   1.095  0.008  0.075 14.916  0.005  4.115   6.7107e-02
   2_bss:   1.095  0.008  0.075 14.916  0.005  4.115   6.7107e-02
   2_xyz:   1.012  0.007  0.074 14.500  0.004  4.126   6.0159e-02
   2_adp:   1.012  0.007  0.074 14.500  0.004  4.126   6.0159e-02
   2_occ:   1.012  0.007  0.074 14.500  0.004  4.126   6.0159e-02
   3_bss:   1.012  0.007  0.074 14.500  0.004  4.126   6.0159e-02
   3_xyz:   1.020  0.008  0.077 14.643  0.004  4.114   6.2888e-02
   3_adp:   1.020  0.008  0.077 14.643  0.004  4.114   6.2888e-02
   3_occ:   1.020  0.008  0.077 14.643  0.004  4.114   6.2888e-02
   4_bss:   1.020  0.008  0.077 14.643  0.004  4.114   6.2888e-02
   4_xyz:   0.922  0.006  0.070 14.366  0.004  4.114   5.2150e-02
   4_adp:   0.922  0.006  0.070 14.366  0.004  4.114   5.2150e-02
   4_occ:   0.922  0.006  0.070 14.366  0.004  4.114   5.2150e-02
   5_bss:   0.922  0.006  0.070 14.366  0.004  4.114   5.2150e-02
   5_xyz:   1.025  0.008  0.077 14.604  0.004  4.115   6.2950e-02
   5_adp:   1.025  0.008  0.077 14.604  0.004  4.115   6.2950e-02
   5_occ:   1.025  0.008  0.077 14.604  0.004  4.115   6.2950e-02
   5_bss:   1.025  0.008  0.077 14.604  0.004  4.115   6.2950e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4179e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4179e-01
   1_xyz:   9.478  0.043  0.301 85.894  0.047  2.333   6.8516e-02
   1_adp:   9.478  0.043  0.301 85.894  0.047  2.333   6.8516e-02
   1_occ:   9.478  0.043  0.301 85.894  0.047  2.333   6.8516e-02
   2_bss:   9.478  0.043  0.301 85.894  0.047  2.333   6.8516e-02
   2_xyz:   8.312  0.039  0.223 81.375  0.035  2.347   7.2434e-02
   2_adp:   8.312  0.039  0.223 81.375  0.035  2.347   7.2434e-02
   2_occ:   8.312  0.039  0.223 81.375  0.035  2.347   7.2434e-02
   3_bss:   8.312  0.039  0.223 81.375  0.035  2.347   7.2434e-02
   3_xyz:   8.198  0.040  0.233 84.296  0.036  2.313   4.3984e-02
   3_adp:   8.198  0.040  0.233 84.296  0.036  2.313   4.3984e-02
   3_occ:   8.198  0.040  0.233 84.296  0.036  2.313   4.3984e-02
   4_bss:   8.198  0.040  0.233 84.296  0.036  2.313   4.3984e-02
   4_xyz:   7.800  0.036  0.205 83.722  0.036  2.386   3.1436e-02
   4_adp:   7.800  0.036  0.205 83.722  0.036  2.386   3.1436e-02
   4_occ:   7.800  0.036  0.205 83.722  0.036  2.386   3.1436e-02
   5_bss:   7.800  0.036  0.205 83.722  0.036  2.386   3.1436e-02
   5_xyz:   7.763  0.040  0.233 84.476  0.036  2.317   4.2919e-02
   5_adp:   7.763  0.040  0.233 84.476  0.036  2.317   4.2919e-02
   5_occ:   7.763  0.040  0.233 84.476  0.036  2.317   4.2919e-02
   5_bss:   7.763  0.040  0.233 84.476  0.036  2.317   4.2919e-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:  63.31   0.00  16.59  55.12   0.00  12.73  63.31   5.07  37.61
   1_occ:  63.31   0.00  16.59  55.12   0.00  12.73  63.31   5.07  37.61
   2_bss:  63.31   0.00  16.59  55.12   0.00  12.73  63.31   5.07  37.61
   2_xyz:  63.31   0.00  16.59  55.12   0.00  12.73  63.31   5.07  37.61
   2_adp:  73.11   1.23  17.05  71.95   1.23  13.05  73.11   6.08  38.83
   2_occ:  73.11   1.23  17.05  71.95   1.23  13.05  73.11   6.08  38.83
   3_bss:  73.11   1.23  17.05  71.95   1.23  13.05  73.11   6.08  38.83
   3_xyz:  73.11   1.23  17.05  71.95   1.23  13.05  73.11   6.08  38.83
   3_adp:  74.82   1.72  16.81  73.32   1.72  12.98  74.82   2.86  37.66
   3_occ:  74.82   1.72  16.81  73.32   1.72  12.98  74.82   2.86  37.66
   4_bss:  74.82   1.72  16.81  73.32   1.72  12.98  74.82   2.86  37.66
   4_xyz:  74.82   1.72  16.81  73.32   1.72  12.98  74.82   2.86  37.66
   4_adp:  77.55   1.04  16.91  77.55   1.04  12.96  76.50   4.14  38.41
   4_occ:  77.55   1.04  16.91  77.55   1.04  12.96  76.50   4.14  38.41
   5_bss:  77.55   1.04  16.91  77.55   1.04  12.96  76.50   4.14  38.41
   5_xyz:  77.55   1.04  16.91  77.55   1.04  12.96  76.50   4.14  38.41
   5_adp:  88.29   0.48  17.14  88.29   0.48  12.96  84.09   5.21  39.92
   5_occ:  88.29   0.48  17.14  88.29   0.48  12.96  84.09   5.21  39.92
   5_bss:  88.27   0.46  17.12  88.27   0.46  12.94  84.08   5.20  39.90
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.189    0.013    0.320
   1_adp:    1.189    0.013    0.320
   1_occ:    1.189    0.013    0.320
   2_bss:    1.189    0.013    0.320
   2_xyz:    0.866    0.029    0.374
   2_adp:    0.866    0.029    0.374
   2_occ:    0.866    0.029    0.374
   3_bss:    0.866    0.029    0.374
   3_xyz:    0.880    0.033    0.401
   3_adp:    0.880    0.033    0.401
   3_occ:    0.880    0.033    0.401
   4_bss:    0.880    0.033    0.401
   4_xyz:    0.910    0.048    0.407
   4_adp:    0.910    0.048    0.407
   4_occ:    0.910    0.048    0.407
   5_bss:    0.910    0.048    0.407
   5_xyz:    0.967    0.059    0.414
   5_adp:    0.967    0.059    0.414
   5_occ:    0.967    0.059    0.414
   5_bss:    0.967    0.059    0.414
------------------------------------------------------------------------

CPU time actual refinement: 348.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/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_1137/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1137/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.26 
  Macro-tasks:
    bulk solvent and scale       = 36.30  
    individual site refinement   = 152.83 
    weights calculation          = 29.29  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 225.01 
  Micro-tasks:
    mask                            = 1.22   
    f_calc                          = 115.23 
    alpha_beta                      = 8.18   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 125.63 
    fmodel                         = 6.81   
    r_factors                      = 0.16   
    phase_errors                   = 10.86  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 269.56 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.810 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    673 calls, 114.94 s
gradients_fft:          618 calls, 111.07 s

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

# Date 2008-01-16 Time 06:31:22 PST -0800 (1200493882.76 s)
Start R-work = 0.3291, R-free = 0.3283 (no bulk solvent and anisotropic scale)
Final R-work = 0.1332, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.3154, R-free = 0.3143
Final R-work = 0.1090, R-free = 0.1582