# Date 2008-01-16 Time 05:37:07 PST -0800 (1200490627.18 s)
#phil __OFF__

Command line arguments: "../811.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8862
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 811

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 87.6859, 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: 3.27, 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: (70.6012, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.01058
Completeness in resolution range: 0.972642
Completeness with d_max=infinity: 0.96956

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.01058
Completeness in resolution range: 0.972642
Completeness with d_max=infinity: 0.96956

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.3015 [2117/2141]  1903   214  10.1%
  bin  2:  4.3015 -  3.4273 [2037/2056]  1836   201   9.9%
  bin  3:  3.4273 -  2.9979 [2007/2026]  1808   199   9.9%
  bin  4:  2.9979 -  2.7256 [1980/2010]  1776   204  10.3%
  bin  5:  2.7256 -  2.5312 [1982/2001]  1787   195   9.8%
  bin  6:  2.5312 -  2.3826 [1963/1988]  1767   196  10.0%
  bin  7:  2.3826 -  2.2636 [1954/1982]  1759   195  10.0%
  bin  8:  2.2636 -  2.1654 [1946/1982]  1751   195  10.0%
  bin  9:  2.1654 -  2.0823 [1929/1971]  1735   194  10.1%
  bin 10:  2.0823 -  2.0106 [1674/1983]  1508   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/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: 2152
        3.04 -     3.66: 4591
        3.66 -     4.28: 8880
        4.28 -     4.90: 12249
  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  42 " - " O   HOH Z 183 "  1.930 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.024 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.135 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.135 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27880 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_811/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3525   r_free= 0.3432   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.103520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.2885 0.2872       6.352      6.2846|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.2717 0.2720      6.4962      6.5232|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.3093 0.2932      6.4361      6.4091|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.3344 0.3460      6.3197      6.2972|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.3618 0.2977      6.1778       6.077|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.3655 0.3880      6.0985       6.074|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.3768 0.3729      6.0582      6.0323|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.3926 0.3517      6.0439      6.0135|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.3934 0.3720      5.9741      5.9608|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.4133 0.3656      6.0093      5.8829|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.4179 0.4014      5.9372      5.9263|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.4124 0.4314      5.8754      5.9856|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.4204 0.3944      5.7989      5.7676|
| 14:  2.0607 -  2.0106 0.78    993  112 0.4088 0.4469      5.7312      5.7277|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.79  26.05   0.85     0.81      42613.26|
|  2:  4.7973 -  3.8281  1311   149  0.83  23.36   0.96     0.89      51149.14|
|  3:  3.8281 -  3.3503  1306   145  0.79  27.47   0.96     0.90      50280.06|
|  4:  3.3503 -  3.0467  1288   136  0.75  30.94   0.96     0.87      44455.07|
|  5:  3.0467 -  2.8298  1269   144  0.69  35.89   0.97     0.84      36111.08|
|  6:  2.8298 -  2.6640  1276   145  0.68  37.46   0.96     0.82      33725.38|
|  7:  2.6640 -  2.5312  1280   141  0.66  39.18   0.98     0.82      31528.49|
|  8:  2.5312 -  2.4215  1261   137  0.67  38.53   0.97     0.85      29382.29|
|  9:  2.4215 -  2.3286  1251   143  0.67  38.59   0.99     0.87      25930.94|
| 10:  2.3286 -  2.2485  1264   136  0.66  38.81   1.01     0.87      24039.81|
| 11:  2.2485 -  2.1784  1259   142  0.64  40.96   0.98     0.86      24566.52|
| 12:  2.1784 -  2.1163  1231   139  0.61  43.46   0.99     0.83      25119.21|
| 13:  2.1163 -  2.0607  1261   137  0.58  46.23   0.99     0.79      23622.25|
| 14:  2.0607 -  2.0106   993   112  0.56  47.55   0.99     0.74      20434.89|
|alpha:            min =        0.74 max =            0.90 mean =         0.84|
|beta:             min =    20434.89 max =        51149.14 mean =     33454.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.95 mean =        36.43|
|phase err.(test): min =        0.00 max =           89.99 mean =        36.23|
|-----------------------------------------------------------------------------|

============================== 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 = 3.423935              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.212   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.785124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.067   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      175 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1977 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1831 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2760 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4564 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4316 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5566 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6683 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.116    4.900  1.806 |       0.154 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3525   r_free= 0.3432   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.103520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3404   r_free= 0.3322   ksol= 0.31   Bsol= 60.21   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,0.16,2.16,0.00,0.00,0.00); trace/3= -0.27                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.082993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.137557              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.053   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457721              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.932   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3404      final r-factor (work) = 0.2176          |
| start r-factor (free) = 0.3322      final r-factor (free) = 0.2379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7119 = 3.14 * 0.50 * 6.0870 + 1.00 * 0.1627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2215 = 3.14 * 0.50 * 5.8338 + 1.00 * 0.0695                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2176      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.2379      final r-factor (free) = 0.2435          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6765 = 0.46 * 1.00 * 5.8338 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5831 = 0.46 * 1.00 * 5.6203 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.97   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    80.97   17.19    None  None   None       |
|    Sol.    : 438    0      4.94    80.97   39.56    None  None   None       |
|    Mac.    : 2385   0      0.00    72.63   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.097:  637   |   5:    40.485 -  48.583:  108        |
|      1:     8.097 -  16.194: 1236   |   6:    48.583 -  56.680:   75        |
|      2:    16.194 -  24.291:  405   |   7:    56.680 -  64.777:   47        |
|      3:    24.291 -  32.388:  163   |   8:    64.777 -  72.874:   28        |
|      4:    32.388 -  40.485:  119   |   9:    72.874 -  80.971:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1981 r_free = 0.2435             target_work(ml) = 5.629         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1976 r_free = 0.2435             target_work(ml) = 5.628         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1976   r_free= 0.2435   ksol= 0.31   Bsol= 60.21   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,0.16,2.16,0.00,0.00,0.00); trace/3= -0.27                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.628237                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1964   r_free= 0.2416   ksol= 0.33   Bsol= 75.30   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.06,0.01,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.624932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.836194              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.394   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1964      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2416      final r-factor (free) = 0.1858          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2323 = 1.84 * 0.50 * 5.6233 + 1.00 * 0.0695                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1112 = 1.84 * 0.50 * 5.5045 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1482      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.1858      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5226 = 0.27 * 1.00 * 5.5045 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4754 = 0.27 * 1.00 * 5.3372 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    81.23   16.92    None  None   None       |
|    all(noH): 2823   0      1.04    81.23   16.92    None  None   None       |
|    Sol.    : 438    0      5.48    81.23   39.74    None  None   None       |
|    Mac.    : 2385   0      1.04    73.38   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:     1.040 -   9.059:  894   |   5:    41.137 -  49.156:  104        |
|      1:     9.059 -  17.079: 1104   |   6:    49.156 -  57.175:   81        |
|      2:    17.079 -  25.098:  322   |   7:    57.175 -  65.195:   43        |
|      3:    25.098 -  33.117:  128   |   8:    65.195 -  73.214:   23        |
|      4:    33.117 -  41.137:  118   |   9:    73.214 -  81.233:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1403 r_free = 0.1774             target_work(ml) = 5.314         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1401 r_free = 0.1773             target_work(ml) = 5.314         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1401   r_free= 0.1773   ksol= 0.33   Bsol= 75.30   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.06,0.01,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.313831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1402   r_free= 0.1770   ksol= 0.33   Bsol= 71.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.39,-0.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.313417                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.875237              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.253   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.429615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.408  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0618 = 1.88 * 0.50 * 5.3372 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9825 = 1.88 * 0.50 * 5.2515 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7683 = 2.43 * 1.00 * 5.2515 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6387 = 2.43 * 1.00 * 5.1971 + 1.00 * 0.0117                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.18   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    92.18   17.21    None  None   None       |
|    Sol.    : 438    0      5.16    84.24   42.17    None  None   None       |
|    Mac.    : 2385   0      0.00    92.18   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.218:  986   |   5:    46.090 -  55.308:   87        |
|      1:     9.218 -  18.436: 1133   |   6:    55.308 -  64.526:   77        |
|      2:    18.436 -  27.654:  238   |   7:    64.526 -  73.744:   40        |
|      3:    27.654 -  36.872:  128   |   8:    73.744 -  82.962:   18        |
|      4:    36.872 -  46.090:  110   |   9:    82.962 -  92.180:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1643             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1642             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1642   ksol= 0.33   Bsol= 71.21   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.39,-0.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.196820                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1641   ksol= 0.33   Bsol= 71.21   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.33,-0.11,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.196609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.870197              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.015  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.063104              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.455  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9185 = 1.87 * 0.50 * 5.1972 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9036 = 1.87 * 0.50 * 5.1810 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5196 = 1.06 * 1.00 * 5.1810 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5108 = 1.06 * 1.00 * 5.1728 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   16.96    None  None   None       |
|    Sol.    : 438    0      5.17    84.71   41.81    None  None   None       |
|    Mac.    : 2385   0      0.00    93.01   12.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.302: 1043   |   5:    46.507 -  55.809:   83        |
|      1:     9.302 -  18.603: 1098   |   6:    55.809 -  65.110:   78        |
|      2:    18.603 -  27.904:  220   |   7:    65.110 -  74.412:   36        |
|      3:    27.904 -  37.206:  135   |   8:    74.412 -  83.713:   16        |
|      4:    37.206 -  46.507:  108   |   9:    83.713 -  93.015:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1621             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1621             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1621   ksol= 0.33   Bsol= 71.21   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.33,-0.11,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.171180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1616   ksol= 0.32   Bsol= 66.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.22,-0.01,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.170496                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.295953              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.335  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.219495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.957  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9978 = 2.30 * 0.50 * 5.1734 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9868 = 2.30 * 0.50 * 5.1565 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.0824 = 6.22 * 1.00 * 5.1565 + 1.00 * 0.0115                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.0698 = 6.22 * 1.00 * 5.1544 + 1.00 * 0.0120                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.48   16.72    None  None   None       |
|    all(noH): 2823   0      0.00    94.48   16.72    None  None   None       |
|    Sol.    : 438    0      4.74    86.26   41.48    None  None   None       |
|    Mac.    : 2385   0      0.00    94.48   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.449: 1135   |   5:    47.242 -  56.691:   87        |
|      1:     9.449 -  18.897: 1023   |   6:    56.691 -  66.139:   71        |
|      2:    18.897 -  28.346:  215   |   7:    66.139 -  75.588:   36        |
|      3:    28.346 -  37.794:  130   |   8:    75.588 -  85.036:   13        |
|      4:    37.794 -  47.242:  108   |   9:    85.036 -  94.485:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1613             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1613             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1613   ksol= 0.32   Bsol= 66.77   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.22,-0.01,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155609                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.0974 0.1284      5.3848       5.518|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.0818 0.1080      5.4119      5.6242|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.1031 0.1487      5.4639      5.8451|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.1179 0.1582      5.4415      5.5962|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.1350 0.1763      5.3492      5.5611|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.1215 0.1977      5.2394       5.518|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.1277 0.1730      5.1827      5.3746|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.1177 0.1710         5.1      5.3817|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.1168 0.1869      5.0475      5.3327|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.1159 0.1852      5.0062      5.2616|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.1173 0.1808      4.9783      5.2368|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.1172 0.1746      4.9212      5.2637|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.1119 0.1853       4.817       5.109|
| 14:  2.0607 -  2.0106 0.78    993  112 0.1016 0.1787       4.675      4.9819|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.94   9.47   0.96     0.93       7494.81|
|  2:  4.7973 -  3.8281  1311   149  0.95   7.88   1.00     0.98       8875.95|
|  3:  3.8281 -  3.3503  1306   145  0.94  10.96   1.02     1.02      10173.22|
|  4:  3.3503 -  3.0467  1288   136  0.92  13.31   1.00     0.98      10095.87|
|  5:  3.0467 -  2.8298  1269   144  0.90  16.09   1.00     0.97       8706.48|
|  6:  2.8298 -  2.6640  1276   145  0.90  16.38   0.98     0.95       7589.18|
|  7:  2.6640 -  2.5312  1280   141  0.90  16.20   0.98     0.95       6567.89|
|  8:  2.5312 -  2.4215  1261   137  0.91  15.25   0.98     0.96       5632.38|
|  9:  2.4215 -  2.3286  1251   143  0.91  15.86   0.99     0.95       5290.78|
| 10:  2.3286 -  2.2485  1264   136  0.89  16.53   0.98     0.93       4787.23|
| 11:  2.2485 -  2.1784  1259   142  0.90  16.62   0.97     0.94       4765.02|
| 12:  2.1784 -  2.1163  1231   139  0.90  16.32   0.99     0.98       4335.01|
| 13:  2.1163 -  2.0607  1261   137  0.90  16.15   0.97     0.95       3567.97|
| 14:  2.0607 -  2.0106   993   112  0.92  14.61   0.94     0.91       2637.79|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2637.79 max =        10173.22 mean =      6558.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.34|
|phase err.(test): min =        0.00 max =           89.25 mean =        13.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1612   ksol= 0.32   Bsol= 66.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-0.99,0.21,-0.00,0.00,0.00); trace/3= -0.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1612   ksol= 0.32   Bsol= 66.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,-0.99,0.21,-0.00,0.00,0.00); trace/3= -0.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155725                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7973 0.99   1380  153 0.0974 0.1285      5.3856      5.5194|
|  2:  4.7973 -  3.8281 0.99   1311  149 0.0819 0.1080      5.4125      5.6242|
|  3:  3.8281 -  3.3503 0.99   1306  145 0.1031 0.1488       5.464      5.8458|
|  4:  3.3503 -  3.0467 0.99   1288  136 0.1178 0.1582      5.4415      5.5964|
|  5:  3.0467 -  2.8298 0.99   1269  144 0.1349 0.1762       5.349      5.5607|
|  6:  2.8298 -  2.6640 0.99   1276  145 0.1214 0.1978      5.2393       5.518|
|  7:  2.6640 -  2.5312 0.99   1280  141 0.1277 0.1730      5.1828      5.3747|
|  8:  2.5312 -  2.4215 0.98   1261  137 0.1178 0.1709      5.1002      5.3817|
|  9:  2.4215 -  2.3286 0.98   1251  143 0.1168 0.1869      5.0476      5.3326|
| 10:  2.3286 -  2.2485 0.99   1264  136 0.1159 0.1853      5.0062      5.2618|
| 11:  2.2485 -  2.1784 0.98   1259  142 0.1173 0.1806      4.9782      5.2361|
| 12:  2.1784 -  2.1163 0.97   1231  139 0.1172 0.1743       4.921      5.2631|
| 13:  2.1163 -  2.0607 1.00   1261  137 0.1119 0.1853      4.8169       5.109|
| 14:  2.0607 -  2.0106 0.78    993  112 0.1016 0.1786      4.6752       4.982|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7973  1380   153  0.94   9.48   0.96     0.94       7514.29|
|  2:  4.7973 -  3.8281  1311   149  0.95   7.89   1.00     0.99       8888.32|
|  3:  3.8281 -  3.3503  1306   145  0.94  10.96   1.02     1.02      10177.42|
|  4:  3.3503 -  3.0467  1288   136  0.92  13.31   1.01     0.99      10095.36|
|  5:  3.0467 -  2.8298  1269   144  0.90  16.08   1.01     0.98       8704.38|
|  6:  2.8298 -  2.6640  1276   145  0.90  16.38   0.99     0.96       7586.95|
|  7:  2.6640 -  2.5312  1280   141  0.90  16.20   0.99     0.96       6568.89|
|  8:  2.5312 -  2.4215  1261   137  0.91  15.26   0.99     0.97       5633.87|
|  9:  2.4215 -  2.3286  1251   143  0.91  15.87   1.00     0.96       5294.02|
| 10:  2.3286 -  2.2485  1264   136  0.89  16.53   0.99     0.94       4785.69|
| 11:  2.2485 -  2.1784  1259   142  0.90  16.62   0.98     0.95       4762.05|
| 12:  2.1784 -  2.1163  1231   139  0.90  16.32   1.00     0.99       4332.82|
| 13:  2.1163 -  2.0607  1261   137  0.90  16.15   0.98     0.96       3567.17|
| 14:  2.0607 -  2.0106   993   112  0.92  14.61   0.96     0.92       2637.64|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2637.64 max =        10177.42 mean =      6561.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.34|
|phase err.(test): min =        0.00 max =           89.25 mean =        13.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.49   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    94.49   16.73    None  None   None       |
|    Sol.    : 438    0      4.74    86.27   41.49    None  None   None       |
|    Mac.    : 2385   0      0.00    94.49   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.452: 1135   |   5:    47.245 -  56.694:   87        |
|      1:     9.452 -  18.900: 1023   |   6:    56.694 -  66.142:   71        |
|      2:    18.900 -  28.348:  215   |   7:    66.142 -  75.591:   36        |
|      3:    28.348 -  37.797:  130   |   8:    75.591 -  85.039:   13        |
|      4:    37.797 -  47.245:  108   |   9:    85.039 -  94.488:    5        |
|                               =>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: 0.485 - 4.902
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.715 - 4.902

peak=    5.700 closest distance to " NH2 ARG A  56 " =    2.283
peak=    5.580 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.020 closest distance to " CG  PRO A  54 " =    1.312
peak=    4.862 closest distance to " CB  GLN A 183 " =    1.263
peak=    4.766 closest distance to " CB  ARG A 190 " =    1.606
peak=    4.758 closest distance to " CZ  PHE A 218 " =    1.091
peak=    4.722 closest distance to " CB  ARG A  79 " =    1.412
peak=    4.707 closest distance to " CB  SER A  63 " =    1.163
peak=    4.569 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.567 closest distance to " O   HOH Z 369 " =    2.256
peak=    4.548 closest distance to " CB  ARG A 275 " =    0.997
peak=    4.532 closest distance to " NE2 GLN A  11 " =    1.019
peak=    4.530 closest distance to " O   HOH Z 126 " =    1.922
peak=    4.456 closest distance to " CG  PRO A 198 " =    1.258
peak=    4.441 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.408 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.404 closest distance to " C   PRO A 198 " =    1.513
peak=    4.383 closest distance to " O   HOH Z 298 " =    1.969
peak=    4.337 closest distance to " O   HOH Z 189 " =    2.791
peak=    4.268 closest distance to " O   HOH Z 142 " =    1.610
peak=    4.239 closest distance to " CB  GLU A 277 " =    3.742
peak=    4.218 closest distance to " O   HOH Z  78 " =    1.630
peak=    4.195 closest distance to " CB  LEU A 228 " =    1.101
peak=    4.171 closest distance to " O   HOH Z 427 " =    3.093
peak=    4.143 closest distance to " O   HOH Z 234 " =    3.840
peak=    4.120 closest distance to " CB  TYR A 169 " =    0.762
peak=    4.111 closest distance to " CB  PRO A  54 " =    0.950
peak=    4.110 closest distance to " O   HOH Z  15 " =    2.172
peak=    4.104 closest distance to " O   HOH Z  19 " =    2.210
peak=    4.101 closest distance to " O   HOH Z  40 " =    1.872
peak=    4.091 closest distance to " CA  ARG A 195 " =    1.247
peak=    4.081 closest distance to " O   HOH Z 303 " =    2.191
peak=    4.063 closest distance to " O   HOH Z 368 " =    2.169
peak=    4.047 closest distance to " O   HOH Z 346 " =    1.629
peak=    4.044 closest distance to " CE  LYS A  76 " =    0.862
peak=    4.038 closest distance to " CG  PRO A  90 " =    1.150
peak=    4.020 closest distance to " ND2 ASN A 187 " =    1.474
peak=    4.008 closest distance to " NZ  LYS A 117 " =    3.214
peak=    4.007 closest distance to " O   HOH Z 287 " =    1.949
peak=    4.002 closest distance to " CB  VAL A 202 " =    1.617
peak=    4.002 closest distance to " CD  ARG A 269 " =    0.955
peak=    4.001 closest distance to " O   HOH Z 158 " =    3.100
peak=    3.984 closest distance to " CB  GLU A 128 " =    1.008
peak=    3.974 closest distance to " CB  ASN A 148 " =    1.405
peak=    3.962 closest distance to " O   HOH Z 265 " =    2.217
peak=    3.955 closest distance to " CA  ARG A  36 " =    1.105
peak=    3.944 closest distance to " CZ3 TRP A 266 " =    1.119
peak=    3.944 closest distance to " CD1 LEU A  96 " =    0.752
peak=    3.935 closest distance to " CB  TRP A 266 " =    1.032
peak=    3.930 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.929 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.925 closest distance to " N   HIS A 108 " =    1.916
peak=    3.914 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.914 closest distance to " CG  PRO A 243 " =    1.064
peak=    3.910 closest distance to " CB  ASP A 140 " =    1.076
peak=    3.909 closest distance to " O   HOH Z 406 " =    1.620
peak=    3.899 closest distance to " CD1 LEU A 300 " =    1.188
peak=    3.890 closest distance to " CD  LYS A 166 " =    1.305
peak=    3.882 closest distance to " CG2 VAL A 257 " =    0.806
peak=    3.872 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.861 closest distance to " CD2 LEU A 297 " =    0.920
peak=    3.861 closest distance to " O   HOH Z 133 " =    2.588
peak=    3.856 closest distance to " CD2 TRP A 179 " =    1.338
peak=    3.853 closest distance to " CB  GLU A 152 " =    1.166
peak=    3.841 closest distance to " NH1AARG A 145 " =    1.325
peak=    3.827 closest distance to " OD1 ASN A  69 " =    2.587
peak=    3.827 closest distance to " O   SER A  87 " =    2.236
peak=    3.822 closest distance to " O   HOH Z 392 " =    2.901
peak=    3.819 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.815 closest distance to " O   HOH Z  44 " =    2.219
peak=    3.812 closest distance to " CA  TYR A  30 " =    1.045
peak=    3.808 closest distance to " O   ASN A  74 " =    1.544
peak=    3.799 closest distance to " O   HOH Z 214 " =    2.248
peak=    3.795 closest distance to " CB  VAL A 265 " =    1.264
peak=    3.790 closest distance to " O   HOH Z 203 " =    1.723
peak=    3.778 closest distance to " O   HOH Z  63 " =    1.960
peak=    3.757 closest distance to " O   HOH Z  59 " =    2.302
peak=    3.756 closest distance to " CA  MET A 105 " =    1.058
peak=    3.754 closest distance to " CA  ALA A 160 " =    0.952
peak=    3.749 closest distance to " CA  ASN A 215 " =    1.080
peak=    3.728 closest distance to " O   HOH Z 271 " =    2.712
peak=    3.723 closest distance to " O   HOH Z  43 " =    1.929
peak=    3.714 closest distance to " OE1 GLN A  55 " =    1.508
peak=    3.713 closest distance to " OG BSER A 164 " =    2.362
peak=    3.710 closest distance to " NH2 ARG A 156 " =    1.196
peak=    3.709 closest distance to " CG  ARG A  66 " =    2.448
peak=    3.708 closest distance to " O   HOH Z 250 " =    1.435
peak=    3.704 closest distance to " O  BHOH Z 338 " =    2.354
peak=    3.701 closest distance to " CG  MET A 185 " =    1.195
peak=    3.696 closest distance to " O   HOH Z 193 " =    1.873
peak=    3.688 closest distance to " O   HOH Z  21 " =    1.846
peak=    3.684 closest distance to " O   HOH Z 316 " =    3.167
peak=    3.674 closest distance to " O   HOH Z   1 " =    2.329
peak=    3.673 closest distance to " CD ALYS A 290 " =    0.996
peak=    3.664 closest distance to " O   HOH Z 147 " =    1.830
peak=    3.660 closest distance to " CB  GLU A  46 " =    0.992
peak=    3.654 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.639 closest distance to " CA  THR A 221 " =    0.972
peak=    3.633 closest distance to " ND2 ASN A 249 " =    1.928
peak=    3.629 closest distance to " O   HOH Z 412 " =    3.833
peak=    3.629 closest distance to " O   HOH Z 280 " =    2.891
peak=    3.619 closest distance to " O   HOH Z 261 " =    1.747
peak=    3.618 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.618 closest distance to " CA  ALA A 154 " =    0.991
peak=    3.608 closest distance to " O   HOH Z 128 " =    2.180
peak=    3.608 closest distance to " O   HOH Z 353 " =    2.649
peak=    3.604 closest distance to " CA  VAL A 125 " =    1.221
peak=    3.585 closest distance to " O   HOH Z 402 " =    1.393
peak=    3.584 closest distance to " NE2 GLN A  77 " =    3.434
peak=    3.583 closest distance to " O   HOH Z  40 " =    1.665
peak=    3.574 closest distance to " CA  ASN A 176 " =    1.807
peak=    3.563 closest distance to " CA  PRO A  54 " =    1.365
peak=    3.563 closest distance to " O   HOH Z  80 " =    1.654
peak=    3.558 closest distance to " O   HOH Z 371 " =    3.194
peak=    3.557 closest distance to " NH2AARG A 275 " =    3.554
peak=    3.551 closest distance to " O   HOH Z 294 " =    1.531
peak=    3.543 closest distance to " CG1BVAL A  72 " =    1.872
peak=    3.542 closest distance to " ND2 ASN A 249 " =    0.851
peak=    3.542 closest distance to " O   ASN A  74 " =    2.008
peak=    3.540 closest distance to " CB  TYR A 116 " =    0.767
peak=    3.532 closest distance to " O   HOH Z 359 " =    1.513
peak=    3.530 closest distance to " CA  ALA A  21 " =    1.199
peak=    3.524 closest distance to " CG  GLN A  11 " =    1.593
peak=    3.523 closest distance to " N   ARG A 156 " =    1.407
peak=    3.521 closest distance to " O   ALA A 165 " =    1.501
peak=    3.520 closest distance to " CZ  PHE A  38 " =    1.245
peak=    3.519 closest distance to " O   HOH Z 193 " =    1.772
peak=    3.515 closest distance to " CA  ALA A 295 " =    1.087
peak=    3.515 closest distance to " O   HOH Z 325 " =    2.356
peak=    3.514 closest distance to " CB  PRO A  90 " =    1.150
peak=    3.498 closest distance to " CG1 ILE A  33 " =    1.207
peak=    3.498 closest distance to " O   HOH Z 423 " =    1.947
peak=    3.495 closest distance to " O   HOH Z 185 " =    1.868
peak=    3.494 closest distance to " CG2 VAL A 197 " =    1.120
peak=    3.492 closest distance to " CG2 ILE A 234 " =    0.916
peak=    3.489 closest distance to " N   ASN A  39 " =    1.326
peak=    3.489 closest distance to " CB  SER A 212 " =    1.089
peak=    3.488 closest distance to " O   HOH Z 290 " =    0.986
peak=    3.485 closest distance to " O   HOH Z 383 " =    2.125
peak=    3.484 closest distance to " O   HOH Z 422 " =    2.698
peak=    3.480 closest distance to " CG2 ILE A 120 " =    1.025
peak=    3.479 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.472 closest distance to " OG BSER A 134 " =    2.799
peak=    3.466 closest distance to " O   HOH Z 148 " =    3.402
peak=    3.465 closest distance to " O   HOH Z 391 " =    2.902
peak=    3.455 closest distance to " O   HOH Z 421 " =    1.742
peak=    3.454 closest distance to " CB  ASP A 298 " =    1.209
peak=    3.453 closest distance to " CA  ALA A 158 " =    1.230
peak=    3.452 closest distance to " O   HOH Z 285 " =    1.748
peak=    3.451 closest distance to " O   TYR A 116 " =    1.338
peak=    3.449 closest distance to " CA  ASN A 217 " =    1.209
peak=    3.448 closest distance to " N   ASN A 127 " =    1.295
peak=    3.447 closest distance to " O   HOH Z 403 " =    1.567
peak=    3.444 closest distance to " OD2 ASP A 298 " =    3.955
peak=    3.443 closest distance to " CG2 THR A 221 " =    1.062
peak=    3.443 closest distance to " O   HOH Z 285 " =    2.526
peak=    3.441 closest distance to " O   HOH Z 248 " =    1.685
peak=    3.438 closest distance to " CB  TRP A 179 " =    1.458
peak=    3.433 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.418 closest distance to " CB  GLN A  88 " =    1.191
peak=    3.418 closest distance to " NE  ARG A  79 " =    1.020
peak=    3.417 closest distance to " O   HOH Z 126 " =    1.635
peak=    3.416 closest distance to " O   HOH Z 299 " =    4.499
peak=    3.414 closest distance to " CA  SER A  87 " =    1.103
peak=    3.403 closest distance to " CB  LEU A  83 " =    0.812
peak=    3.402 closest distance to " CA  MET A  40 " =    1.158
peak=    3.402 closest distance to " O   THR A 251 " =    1.110
peak=    3.398 closest distance to " O   HOH Z 213 " =    1.913
peak=    3.397 closest distance to " CG  LEU A 167 " =    1.214
peak=    3.395 closest distance to " CB  ALA A 248 " =    1.254
peak=    3.388 closest distance to " O   HOH Z  97 " =    1.985
peak=    3.385 closest distance to " O   THR A 182 " =    1.421
peak=    3.383 closest distance to " CB  ILE A 120 " =    1.252
peak=    3.379 closest distance to " O   HOH Z 272 " =    1.881
peak=    3.377 closest distance to " O   HOH Z 426 " =    1.618
peak=    3.373 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.373 closest distance to " O   HOH Z 106 " =    4.077
peak=    3.372 closest distance to " CA  ASP A 162 " =    1.092
peak=    3.368 closest distance to " CB  THR A  31 " =    1.733
peak=    3.361 closest distance to " NE2 HIS A 207 " =    1.207
peak=    3.361 closest distance to " OG  SER A  22 " =    2.742
peak=    3.359 closest distance to " NZ  LYS A  48 " =    1.260
peak=    3.358 closest distance to " O   HOH Z  88 " =    3.732
peak=    3.355 closest distance to " CB  SER A 141 " =    1.048
peak=    3.349 closest distance to " O   HOH Z 128 " =    2.417
peak=    3.345 closest distance to " CA  ASN A 127 " =    1.190
peak=    3.341 closest distance to " O   HOH Z 261 " =    1.753
peak=    3.338 closest distance to " CA  ASP A 124 " =    0.718
peak=    3.327 closest distance to " CA  ALA A 233 " =    1.586
peak=    3.326 closest distance to " O   ASP A 191 " =    1.536
peak=    3.324 closest distance to " CA  GLY A 241 " =    0.836
peak=    3.323 closest distance to " O   HOH Z 425 " =    2.037
peak=    3.321 closest distance to " O   HOH Z 291 " =    1.513
peak=    3.321 closest distance to " O   HOH Z 305 " =    3.687
peak=    3.318 closest distance to " CG  GLU A  37 " =    0.895
peak=    3.316 closest distance to " CB  ALA A 291 " =    1.283
peak=    3.315 closest distance to " CB  ALA A   1 " =    4.902
peak=    3.314 closest distance to " CA  TYR A 116 " =    1.416
peak=    3.314 closest distance to " OH  TYR A 116 " =    1.091
peak=    3.311 closest distance to " O   HOH Z 365 " =    2.873
peak=    3.310 closest distance to " CB  ALA A 248 " =    1.001
peak=    3.309 closest distance to " CB  LYS A 117 " =    1.207
peak=    3.300 closest distance to " CB  MET A  47 " =    0.979
peak=    3.298 closest distance to " O   HOH Z  62 " =    2.270
peak=    3.296 closest distance to " O   ASP A 124 " =    1.275
peak=    3.290 closest distance to " CG2 ILE A  20 " =    1.250
peak=    3.285 closest distance to " O   HOH Z 279 " =    2.293
peak=    3.285 closest distance to " O   HOH Z 313 " =    1.851
peak=    3.283 closest distance to " O   HOH Z 425 " =    1.282
peak=    3.280 closest distance to " CB  SER A   3 " =    1.401
peak=    3.275 closest distance to " CA  ALA A 291 " =    0.749
peak=    3.272 closest distance to " CB  THR A  82 " =    1.466
peak=    3.270 closest distance to " CA  LEU A  83 " =    1.226
peak=    3.269 closest distance to " CB  SER A  62 " =    0.715
peak=    3.269 closest distance to " O   HOH Z  90 " =    2.312
peak=    3.261 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.261 closest distance to " CB  ARG A 138 " =    0.973
peak=    3.259 closest distance to " O   HOH Z  44 " =    1.648
peak=    3.258 closest distance to " O   HOH Z 327 " =    1.512
peak=    3.257 closest distance to " OG  SER A 245 " =    1.690
peak=    3.255 closest distance to " NH2BARG A 145 " =    2.192
peak=    3.254 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.248 closest distance to " O   HOH Z 417 " =    3.024
peak=    3.248 closest distance to " N   ASN A 252 " =    1.316
peak=    3.247 closest distance to " CG  PHE A 204 " =    0.815
peak=    3.245 closest distance to " ND1 HIS A  81 " =    1.639
peak=    3.242 closest distance to " CB  GLN A 103 " =    0.854
peak=    3.237 closest distance to " O   HOH Z 371 " =    3.419
peak=    3.236 closest distance to " CA  THR A 264 " =    0.910
peak=    3.234 closest distance to " CB  GLN A 205 " =    1.100
peak=    3.231 closest distance to " O   HOH Z 174 " =    2.426
peak=    3.230 closest distance to " O   HOH Z 130 " =    2.995
peak=    3.230 closest distance to " O   HOH Z 134 " =    1.158
peak=    3.229 closest distance to " CG2 THR A  29 " =    1.331
peak=    3.228 closest distance to " O   HOH Z 245 " =    1.267
peak=    3.227 closest distance to " O   THR A 220 " =    1.209
peak=    3.227 closest distance to " CB  ALA A   9 " =    1.599
peak=    3.223 closest distance to " O   HOH Z 163 " =    1.894
peak=    3.220 closest distance to " CA  MET A 188 " =    0.984
peak=    3.219 closest distance to " O   HOH Z 258 " =    2.053
peak=    3.217 closest distance to " O   HOH Z 193 " =    2.195
peak=    3.216 closest distance to " O   HOH Z 171 " =    3.979
peak=    3.213 closest distance to " CA  LYS A 117 " =    1.220
peak=    3.204 closest distance to " O   HOH Z  68 " =    2.157
peak=    3.204 closest distance to " NE2 HIS A 115 " =    0.988
peak=    3.197 closest distance to " O   HOH Z 258 " =    1.667
peak=    3.196 closest distance to " CA  GLU A  46 " =    0.789
peak=    3.193 closest distance to " N   TYR A 116 " =    1.585
peak=    3.189 closest distance to " CA  ALA A 100 " =    1.039
peak=    3.188 closest distance to " OD1 ASN A 301 " =    1.627
peak=    3.188 closest distance to " O   THR A 251 " =    1.878
peak=    3.187 closest distance to " O   HOH Z 344 " =    3.219
peak=    3.186 closest distance to " O   HOH Z 273 " =    2.876
peak=    3.183 closest distance to " CB  THR A  52 " =    0.757
peak=    3.183 closest distance to " CZ2 TRP A 179 " =    1.730
peak=    3.181 closest distance to " O   HOH Z  48 " =    1.724
peak=    3.174 closest distance to " O   HOH Z  20 " =    1.518
peak=    3.173 closest distance to " O   ALA A 158 " =    1.167
peak=    3.169 closest distance to " O   HOH Z 251 " =    1.548
peak=    3.168 closest distance to " N   PHE A 130 " =    1.243
peak=    3.167 closest distance to " CB  ASN A 285 " =    0.950
peak=    3.165 closest distance to " N   VAL A 126 " =    1.456
peak=    3.162 closest distance to " CE  LYS A  48 " =    1.046
peak=    3.160 closest distance to " O   HOH Z 282 " =    1.948
peak=    3.159 closest distance to " CG BARG A 275 " =    1.336
peak=    3.153 closest distance to " O   HOH Z 156 " =    2.635
peak=    3.153 closest distance to " CA  ALA A  84 " =    1.270
peak=    3.150 closest distance to " CB  PHE A 204 " =    0.786
peak=    3.149 closest distance to " N   CYS A 260 " =    0.820
peak=    3.139 closest distance to " CA  ARG A 139 " =    1.042
peak=    3.139 closest distance to " CG2AVAL A 121 " =    2.262
peak=    3.134 closest distance to " CG BARG A 102 " =    1.854
peak=    3.133 closest distance to " CA  GLU A 152 " =    0.882
peak=    3.128 closest distance to " OG  SER A  62 " =    2.936
peak=    3.127 closest distance to " CB  ASN A 215 " =    1.207
peak=    3.127 closest distance to " CB  ALA A  43 " =    0.802
peak=    3.125 closest distance to " CG2 THR A 220 " =    0.970
peak=    3.120 closest distance to " CB  ALA A 104 " =    0.735
peak=    3.117 closest distance to " CA  ARG A 159 " =    1.281
peak=    3.115 closest distance to " CA  ARG A 102 " =    1.109
peak=    3.110 closest distance to " CA  ASP A 191 " =    0.891
peak=    3.103 closest distance to " O   HOH Z 419 " =    1.942
peak=    3.098 closest distance to " N   TYR A 247 " =    1.107
peak=    3.097 closest distance to " CA  ASP A 191 " =    1.201
peak=    3.095 closest distance to " CG  ARG A 219 " =    1.092
peak=    3.090 closest distance to " O   HOH Z 116 " =    1.787
peak=    3.083 closest distance to " CA  ILE A 106 " =    0.829
peak=    3.074 closest distance to " CA  ASP A 140 " =    1.252
peak=    3.060 closest distance to " CB  ASN A 187 " =    1.081
peak=    3.058 closest distance to " CA  GLY A 211 " =    1.295
peak=    3.058 closest distance to " O   GLU A   2 " =    1.781
peak=    3.056 closest distance to " O   HOH Z  96 " =    2.218
peak=    3.021 closest distance to " OG BSER A  99 " =    2.305

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.991 - 5.907
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 207
   mapped sites are within: 0.991 - 5.907

peak=   -4.631 closest distance to " CD  GLN A  58 " =    1.004
peak=   -4.585 closest distance to " O   HOH Z 266 " =    5.424
peak=   -4.540 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -4.433 closest distance to " CD  ARG A  14 " =    3.418
peak=   -4.397 closest distance to " CD  ARG A 156 " =    2.035
peak=   -4.352 closest distance to " O   HOH Z  10 " =    1.527
peak=   -4.308 closest distance to " CB  PRO A 243 " =    2.653
peak=   -4.249 closest distance to " O   HOH Z 231 " =    2.302
peak=   -4.235 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.217 closest distance to " O   VAL A  67 " =    2.689
peak=   -4.209 closest distance to " OG BSER A 134 " =    1.317
peak=   -4.156 closest distance to " O   HOH Z 196 " =    2.086
peak=   -4.072 closest distance to " CD2 TYR A 293 " =    1.999
peak=   -4.061 closest distance to " CG2 ILE A  49 " =    2.774
peak=   -4.044 closest distance to " CB  ALA A 161 " =    2.604
peak=   -4.031 closest distance to " CG1 VAL A 250 " =    2.691
peak=   -4.021 closest distance to " O   HOH Z 377 " =    2.028
peak=   -4.015 closest distance to " CE2 PHE A  61 " =    2.643
peak=   -4.008 closest distance to " O   HOH Z 198 " =    2.052
peak=   -3.998 closest distance to " OG  SER A  97 " =    2.255
peak=   -3.990 closest distance to " O   HOH Z  73 " =    2.306
peak=   -3.984 closest distance to " OE1 GLN A 223 " =    1.967
peak=   -3.971 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.961 closest distance to " CE2 TYR A  30 " =    2.705
peak=   -3.954 closest distance to " OXT GLY A 302 " =    3.029
peak=   -3.893 closest distance to " CZ3 TRP A 179 " =    1.184
peak=   -3.892 closest distance to " CG1 VAL A 112 " =    2.827
peak=   -3.878 closest distance to " CD1 LEU A 101 " =    2.437
peak=   -3.843 closest distance to " N   ALA A  43 " =    2.594
peak=   -3.817 closest distance to " CD  GLN A 223 " =    1.283
peak=   -3.796 closest distance to " OD1 ASN A 148 " =    1.480
peak=   -3.794 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.746 closest distance to " NE2 GLN A 194 " =    1.894
peak=   -3.744 closest distance to " CG  ARG A 269 " =    2.510
peak=   -3.737 closest distance to " CA  VAL A  67 " =    2.947
peak=   -3.733 closest distance to " CA  GLY A 241 " =    3.291
peak=   -3.726 closest distance to " ND2 ASN A  45 " =    1.872
peak=   -3.717 closest distance to " O   HOH Z   6 " =    2.292
peak=   -3.699 closest distance to " O   HOH Z 290 " =    1.213
peak=   -3.699 closest distance to " CB  ASN A  39 " =    2.410
peak=   -3.696 closest distance to " CD1 ILE A 151 " =    2.418
peak=   -3.687 closest distance to " O   HOH Z 128 " =    2.605
peak=   -3.683 closest distance to " O   HOH Z 185 " =    2.332
peak=   -3.682 closest distance to " CD1 PHE A  59 " =    1.990
peak=   -3.680 closest distance to " CG  GLN A  11 " =    1.768
peak=   -3.674 closest distance to " ND2 ASN A  45 " =    1.158
peak=   -3.674 closest distance to " CG  GLU A 277 " =    1.133
peak=   -3.672 closest distance to " O   SER A 210 " =    1.942
peak=   -3.666 closest distance to " O   ALA A  34 " =    2.417
peak=   -3.650 closest distance to " CE3 TRP A 150 " =    2.198
peak=   -3.646 closest distance to " O   HOH Z 394 " =    1.543
peak=   -3.631 closest distance to " O   PRO A 163 " =    2.156
peak=   -3.611 closest distance to " O   HOH Z 292 " =    4.700
peak=   -3.580 closest distance to " O   PHE A 218 " =    1.530
peak=   -3.578 closest distance to " CG  ARG A  66 " =    2.463
peak=   -3.567 closest distance to " O   HOH Z   6 " =    1.517
peak=   -3.566 closest distance to " CG2 ILE A 263 " =    2.367
peak=   -3.552 closest distance to " NH2 ARG A  79 " =    1.516
peak=   -3.550 closest distance to " NE2 GLN A  88 " =    1.902
peak=   -3.547 closest distance to " O   HOH Z 393 " =    1.377
peak=   -3.545 closest distance to " ND2BASN A 224 " =    1.783
peak=   -3.544 closest distance to " CG  PRO A 243 " =    1.781
peak=   -3.542 closest distance to " O   HOH Z 348 " =    2.254
peak=   -3.539 closest distance to " O   HOH Z 114 " =    3.207
peak=   -3.537 closest distance to " CA  GLY A 203 " =    2.413
peak=   -3.531 closest distance to " CG2 VAL A 189 " =    2.213
peak=   -3.522 closest distance to " O   HOH Z  51 " =    1.826
peak=   -3.518 closest distance to " N   THR A  52 " =    1.674
peak=   -3.518 closest distance to " O   HOH Z 166 " =    1.862
peak=   -3.510 closest distance to " CG1 VAL A 125 " =    1.976
peak=   -3.507 closest distance to " O   HOH Z 211 " =    1.575
peak=   -3.501 closest distance to " O   HOH Z 372 " =    2.436
peak=   -3.483 closest distance to " NH2AARG A 275 " =    5.336
peak=   -3.481 closest distance to " CE  MET A 105 " =    2.514
peak=   -3.471 closest distance to " OD1 ASP A 171 " =    1.567
peak=   -3.469 closest distance to " O   HOH Z 111 " =    1.537
peak=   -3.464 closest distance to " O   HOH Z 353 " =    2.203
peak=   -3.463 closest distance to " CB  PHE A 192 " =    2.049
peak=   -3.463 closest distance to " ND2 ASN A  69 " =    1.761
peak=   -3.460 closest distance to " CA  GLY A 133 " =    2.376
peak=   -3.460 closest distance to " O   HOH Z 102 " =    1.518
peak=   -3.456 closest distance to " N   THR A 264 " =    1.378
peak=   -3.455 closest distance to " CB  ASP A 132 " =    2.356
peak=   -3.451 closest distance to " C   GLY A  17 " =    1.189
peak=   -3.450 closest distance to " O   HOH Z 264 " =    1.783
peak=   -3.449 closest distance to " OG BSER A 134 " =    1.973
peak=   -3.447 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.446 closest distance to " O   HOH Z  38 " =    1.444
peak=   -3.445 closest distance to " O   ALA A  10 " =    1.687
peak=   -3.443 closest distance to " CB  ALA A 291 " =    2.371
peak=   -3.443 closest distance to " C   LEU A 143 " =    1.128
peak=   -3.439 closest distance to " CA  GLY A 241 " =    2.350
peak=   -3.435 closest distance to " CB  ALA A  43 " =    2.657
peak=   -3.429 closest distance to " OD1 ASP A 191 " =    1.621
peak=   -3.427 closest distance to " O   HOH Z  60 " =    2.288
peak=   -3.421 closest distance to " CG  HIS A  86 " =    1.113
peak=   -3.413 closest distance to " CG1AVAL A  41 " =    2.708
peak=   -3.407 closest distance to " CD  ARG A  79 " =    1.157
peak=   -3.404 closest distance to " O   HOH Z 407 " =    3.236
peak=   -3.401 closest distance to " O   HOH Z  71 " =    2.188
peak=   -3.392 closest distance to " ND2 ASN A 249 " =    2.445
peak=   -3.381 closest distance to " CB  PHE A  16 " =    2.498
peak=   -3.377 closest distance to " O   HOH Z 326 " =    5.080
peak=   -3.374 closest distance to " CZ  PHE A 155 " =    1.265
peak=   -3.373 closest distance to " CE BMET A  47 " =    1.977
peak=   -3.365 closest distance to " O   HOH Z 177 " =    1.695
peak=   -3.365 closest distance to " O   HOH Z 357 " =    2.049
peak=   -3.361 closest distance to " CB  ALA A 291 " =    2.283
peak=   -3.360 closest distance to " O   HOH Z  44 " =    2.261
peak=   -3.355 closest distance to " O   HOH Z 193 " =    1.732
peak=   -3.355 closest distance to " N   ALA A 226 " =    2.048
peak=   -3.347 closest distance to " O   SER A 135 " =    1.477
peak=   -3.343 closest distance to " O   HOH Z 389 " =    1.936
peak=   -3.343 closest distance to " O   HOH Z 166 " =    1.607
peak=   -3.342 closest distance to " O   HOH Z 216 " =    1.521
peak=   -3.341 closest distance to " O   HOH Z 322 " =    1.362
peak=   -3.339 closest distance to " SG ACYS A 201 " =    2.208
peak=   -3.333 closest distance to " C   ASN A 187 " =    1.944
peak=   -3.333 closest distance to " CB  ALA A 248 " =    2.326
peak=   -3.328 closest distance to " NH2 ARG A  66 " =    2.179
peak=   -3.326 closest distance to " O   HOH Z 265 " =    2.365
peak=   -3.310 closest distance to " CG  MET A 105 " =    0.991
peak=   -3.309 closest distance to " NH2 ARG A 159 " =    2.385
peak=   -3.309 closest distance to " CD2 PHE A 225 " =    1.177
peak=   -3.301 closest distance to " OD2 ASP A 191 " =    1.534
peak=   -3.300 closest distance to " CE3 TRP A  70 " =    1.803
peak=   -3.298 closest distance to " O   HOH Z 421 " =    3.384
peak=   -3.295 closest distance to " O   HOH Z 253 " =    4.180
peak=   -3.293 closest distance to " O   TYR A 186 " =    1.821
peak=   -3.285 closest distance to " C   SER A 206 " =    1.456
peak=   -3.285 closest distance to " O   HOH Z  37 " =    1.819
peak=   -3.282 closest distance to " OH  TYR A 247 " =    1.803
peak=   -3.278 closest distance to " O   HOH Z  43 " =    1.608
peak=   -3.275 closest distance to " C   ALA A 158 " =    1.349
peak=   -3.274 closest distance to " O   HOH Z 275 " =    1.883
peak=   -3.270 closest distance to " O   HOH Z 292 " =    1.844
peak=   -3.265 closest distance to " OE1 GLN A  88 " =    1.033
peak=   -3.264 closest distance to " ND2 ASN A 187 " =    1.639
peak=   -3.264 closest distance to " CD  ARG A 139 " =    1.636
peak=   -3.261 closest distance to " CG  GLU A  53 " =    1.549
peak=   -3.260 closest distance to " CD1 ILE A 239 " =    2.047
peak=   -3.258 closest distance to " N   ALA A 248 " =    1.680
peak=   -3.256 closest distance to " CB  ALA A 248 " =    2.159
peak=   -3.244 closest distance to " O   HOH Z 311 " =    3.792
peak=   -3.242 closest distance to " CG  PHE A 283 " =    2.642
peak=   -3.241 closest distance to " OD2 ASP A 171 " =    1.819
peak=   -3.231 closest distance to " O   HOH Z 351 " =    1.597
peak=   -3.231 closest distance to " O   HOH Z 322 " =    1.684
peak=   -3.227 closest distance to " O   PRO A 198 " =    1.848
peak=   -3.226 closest distance to " O   HOH Z  52 " =    1.575
peak=   -3.226 closest distance to " O   HOH Z 256 " =    2.426
peak=   -3.224 closest distance to " O   SER A  95 " =    1.749
peak=   -3.224 closest distance to " NE2 GLN A  88 " =    1.035
peak=   -3.211 closest distance to " OG BSER A 210 " =    1.508
peak=   -3.207 closest distance to " CB  PRO A  54 " =    2.510
peak=   -3.206 closest distance to " O   HOH Z 139 " =    3.015
peak=   -3.205 closest distance to " O   HOH Z 200 " =    1.754
peak=   -3.204 closest distance to " O   HOH Z 106 " =    1.939
peak=   -3.202 closest distance to " OE2 GLU A   2 " =    1.831
peak=   -3.201 closest distance to " CB  TRP A  85 " =    2.467
peak=   -3.200 closest distance to " O   HOH Z 295 " =    1.618
peak=   -3.199 closest distance to " O   SER A 276 " =    1.697
peak=   -3.196 closest distance to " CZ  TYR A 169 " =    1.835
peak=   -3.192 closest distance to " O   HOH Z 252 " =    4.029
peak=   -3.189 closest distance to " CG  LEU A  83 " =    2.076
peak=   -3.187 closest distance to " CD  GLU A 236 " =    1.114
peak=   -3.183 closest distance to " O   HOH Z  13 " =    1.764
peak=   -3.178 closest distance to " CA  GLY A 241 " =    2.879
peak=   -3.174 closest distance to " O   HOH Z 191 " =    5.907
peak=   -3.169 closest distance to " O   VAL A 189 " =    1.666
peak=   -3.165 closest distance to " ND2 ASN A  60 " =    1.294
peak=   -3.164 closest distance to " O   HOH Z 174 " =    3.810
peak=   -3.162 closest distance to " CE3 TRP A 274 " =    2.479
peak=   -3.160 closest distance to " O   GLY A  80 " =    2.666
peak=   -3.159 closest distance to " O   HOH Z 156 " =    3.637
peak=   -3.154 closest distance to " CB  ASP A 286 " =    1.830
peak=   -3.153 closest distance to " O   HOH Z 171 " =    2.084
peak=   -3.151 closest distance to " NH2BARG A 275 " =    2.120
peak=   -3.151 closest distance to " O   HOH Z 435 " =    2.721
peak=   -3.133 closest distance to " CG1BVAL A  41 " =    2.778
peak=   -3.130 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.130 closest distance to " O   HOH Z 236 " =    1.500
peak=   -3.128 closest distance to " CZ  PHE A  59 " =    1.794
peak=   -3.127 closest distance to " OE1 GLN A 183 " =    1.574
peak=   -3.124 closest distance to " O   HOH Z 317 " =    2.171
peak=   -3.121 closest distance to " O   HOH Z 234 " =    4.407
peak=   -3.112 closest distance to " C   GLY A 262 " =    2.113
peak=   -3.112 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.108 closest distance to " O   HOH Z 323 " =    1.520
peak=   -3.104 closest distance to " CG1BVAL A  72 " =    2.378
peak=   -3.100 closest distance to " CZ  PHE A  38 " =    1.971
peak=   -3.099 closest distance to " CB  TYR A  15 " =    2.240
peak=   -3.097 closest distance to " CB  ALA A  10 " =    2.226
peak=   -3.094 closest distance to " OD1 ASN A 301 " =    2.025
peak=   -3.092 closest distance to " CD1 TRP A  70 " =    1.118
peak=   -3.088 closest distance to " O   GLN A 240 " =    2.557
peak=   -3.084 closest distance to " CD  PRO A 243 " =    2.129
peak=   -3.074 closest distance to " O   HOH Z  64 " =    1.662
peak=   -3.073 closest distance to " CG1 VAL A  78 " =    2.695
peak=   -3.068 closest distance to " O   HOH Z 283 " =    5.521
peak=   -3.063 closest distance to " CG  GLN A  58 " =    1.218
peak=   -3.053 closest distance to " CD  PRO A 213 " =    2.152
peak=   -3.053 closest distance to " O   HOH Z 414 " =    1.579
peak=   -3.042 closest distance to " N   SER A 276 " =    1.451
peak=   -3.030 closest distance to " O   ARG A  24 " =    1.597
peak=   -3.021 closest distance to " O   HOH Z 357 " =    2.231
peak=   -3.012 closest distance to " CG  PRO A 163 " =    2.331

================= 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    :  0.3525 0.3432   6.103520e+00   6.078166e+00
   1_bss:  0.3404 0.3322   6.082993e+00   6.054987e+00
   1_xyz:  0.2176 0.2379   5.685307e+00   5.761724e+00
   1_adp:  0.1981 0.2435   5.628857e+00   5.787127e+00
   1_occ:  0.1976 0.2435   5.628237e+00   5.787791e+00
   2_bss:  0.1964 0.2416   5.624932e+00   5.784086e+00
   2_xyz:  0.1482 0.1858   5.364588e+00   5.549994e+00
   2_adp:  0.1403 0.1774   5.314432e+00   5.504103e+00
   2_occ:  0.1401 0.1773   5.313831e+00   5.504141e+00
   3_bss:  0.1402 0.1770   5.313417e+00   5.501900e+00
   3_xyz:  0.1233 0.1645   5.212240e+00   5.428680e+00
   3_adp:  0.1200 0.1643   5.196930e+00   5.424162e+00
   3_occ:  0.1199 0.1642   5.196820e+00   5.424112e+00
   4_bss:  0.1198 0.1641   5.196609e+00   5.424080e+00
   4_xyz:  0.1159 0.1628   5.175788e+00   5.415562e+00
   4_adp:  0.1154 0.1621   5.171045e+00   5.411687e+00
   4_occ:  0.1154 0.1621   5.171180e+00   5.412024e+00
   5_bss:  0.1154 0.1616   5.170496e+00   5.409701e+00
   5_xyz:  0.1120 0.1616   5.156922e+00   5.409521e+00
   5_adp:  0.1118 0.1613   5.155469e+00   5.409661e+00
   5_occ:  0.1117 0.1613   5.155609e+00   5.410010e+00
   5_bss:  0.1116 0.1612   5.155725e+00   5.410087e+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:  0.312  60.215  -3.134   0.164   2.163   0.000   0.000   0.000
   1_xyz:  0.312  60.215  -3.134   0.164   2.163   0.000   0.000   0.000
   1_adp:  0.312  60.215  -3.134   0.164   2.163   0.000   0.000   0.000
   1_occ:  0.312  60.215  -3.134   0.164   2.163   0.000   0.000   0.000
   2_bss:  0.332  75.303  -2.731  -1.064   0.009  -0.000   0.000   0.000
   2_xyz:  0.332  75.303  -2.731  -1.064   0.009  -0.000   0.000   0.000
   2_adp:  0.332  75.303  -2.731  -1.064   0.009  -0.000   0.000   0.000
   2_occ:  0.332  75.303  -2.731  -1.064   0.009  -0.000   0.000   0.000
   3_bss:  0.332  71.209  -2.339  -1.389  -0.120  -0.000  -0.000  -0.000
   3_xyz:  0.332  71.209  -2.339  -1.389  -0.120  -0.000  -0.000  -0.000
   3_adp:  0.332  71.209  -2.339  -1.389  -0.120  -0.000  -0.000  -0.000
   3_occ:  0.332  71.209  -2.339  -1.389  -0.120  -0.000  -0.000  -0.000
   4_bss:  0.332  71.209  -1.994  -1.330  -0.115  -0.000  -0.000  -0.000
   4_xyz:  0.332  71.209  -1.994  -1.330  -0.115  -0.000  -0.000  -0.000
   4_adp:  0.332  71.209  -1.994  -1.330  -0.115  -0.000  -0.000  -0.000
   4_occ:  0.332  71.209  -1.994  -1.330  -0.115  -0.000  -0.000  -0.000
   5_bss:  0.324  66.770  -1.750  -1.221  -0.014  -0.000  -0.000  -0.000
   5_xyz:  0.324  66.770  -1.750  -1.221  -0.014  -0.000  -0.000  -0.000
   5_adp:  0.324  66.770  -1.750  -1.221  -0.014  -0.000  -0.000  -0.000
   5_occ:  0.324  66.770  -1.750  -1.221  -0.014  -0.000  -0.000  -0.000
   5_bss:  0.324  66.773  -1.466  -0.989   0.206  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.411 0.6876  0.8425    33453.995
   1_bss:  35.466 0.6970  0.8492    30884.396
   1_xyz:  23.292 0.8302  0.9702    14455.699
   1_adp:  24.198 0.8203  0.9544    15362.097
   1_occ:  24.223 0.8200  0.9537    15374.323
   2_bss:  23.956 0.8230  0.9255    15210.764
   2_xyz:  17.663 0.8833  0.9662     8815.008
   2_adp:  16.358 0.8955  0.9629     7971.065
   2_occ:  16.349 0.8956  0.9629     7974.750
   3_bss:  16.283 0.8961  0.9626     7917.499
   3_xyz:  14.784 0.9086  0.9699     6841.787
   3_adp:  14.655 0.9100  0.9605     6776.075
   3_occ:  14.653 0.9100  0.9605     6774.643
   4_bss:  14.648 0.9100  0.9654     6776.509
   4_xyz:  14.427 0.9118  0.9677     6634.342
   4_adp:  14.307 0.9129  0.9604     6576.535
   4_occ:  14.313 0.9129  0.9603     6578.610
   5_bss:  14.280 0.9131  0.9654     6530.280
   5_xyz:  14.300 0.9129  0.9661     6572.250
   5_adp:  14.283 0.9131  0.9573     6556.170
   5_occ:  14.286 0.9131  0.9572     6558.518
   5_bss:  14.289 0.9130  0.9657     6560.795
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.116   1.6271e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.116   1.6271e-01
   1_xyz:   1.127  0.008  0.070 15.014  0.004  4.113   6.9525e-02
   1_adp:   1.127  0.008  0.070 15.014  0.004  4.113   6.9525e-02
   1_occ:   1.127  0.008  0.070 15.014  0.004  4.113   6.9525e-02
   2_bss:   1.127  0.008  0.070 15.014  0.004  4.113   6.9525e-02
   2_xyz:   0.998  0.007  0.075 14.286  0.004  4.128   5.7524e-02
   2_adp:   0.998  0.007  0.075 14.286  0.004  4.128   5.7524e-02
   2_occ:   0.998  0.007  0.075 14.286  0.004  4.128   5.7524e-02
   3_bss:   0.998  0.007  0.075 14.286  0.004  4.128   5.7524e-02
   3_xyz:   0.985  0.008  0.074 14.468  0.004  4.114   5.8602e-02
   3_adp:   0.985  0.008  0.074 14.468  0.004  4.114   5.8602e-02
   3_occ:   0.985  0.008  0.074 14.468  0.004  4.114   5.8602e-02
   4_bss:   0.985  0.008  0.074 14.468  0.004  4.114   5.8602e-02
   4_xyz:   0.987  0.008  0.076 14.386  0.004  4.118   5.8825e-02
   4_adp:   0.987  0.008  0.076 14.386  0.004  4.118   5.8825e-02
   4_occ:   0.987  0.008  0.076 14.386  0.004  4.118   5.8825e-02
   5_bss:   0.987  0.008  0.076 14.386  0.004  4.118   5.8825e-02
   5_xyz:   1.056  0.010  0.080 14.532  0.004  4.122   6.7301e-02
   5_adp:   1.056  0.010  0.080 14.532  0.004  4.122   6.7301e-02
   5_occ:   1.056  0.010  0.080 14.532  0.004  4.122   6.7301e-02
   5_bss:   1.056  0.010  0.080 14.532  0.004  4.122   6.7301e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4371e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4371e-01
   1_xyz:   7.339  0.044  0.290 82.805  0.039  2.206   7.1977e-02
   1_adp:   7.339  0.044  0.290 82.805  0.039  2.206   7.1977e-02
   1_occ:   7.339  0.044  0.290 82.805  0.039  2.206   7.1977e-02
   2_bss:   7.339  0.044  0.290 82.805  0.039  2.206   7.1977e-02
   2_xyz:   6.797  0.049  0.219 81.929  0.044  2.381   1.0159e-01
   2_adp:   6.797  0.049  0.219 81.929  0.044  2.381   1.0159e-01
   2_occ:   6.797  0.049  0.219 81.929  0.044  2.381   1.0159e-01
   3_bss:   6.797  0.049  0.219 81.929  0.044  2.381   1.0159e-01
   3_xyz:   7.177  0.041  0.221 82.805  0.039  2.365   3.6867e-02
   3_adp:   7.177  0.041  0.221 82.805  0.039  2.365   3.6867e-02
   3_occ:   7.177  0.041  0.221 82.805  0.039  2.365   3.6867e-02
   4_bss:   7.177  0.041  0.221 82.805  0.039  2.365   3.6867e-02
   4_xyz:   7.137  0.043  0.245 82.138  0.037  2.399   3.9851e-02
   4_adp:   7.137  0.043  0.245 82.138  0.037  2.399   3.9851e-02
   4_occ:   7.137  0.043  0.245 82.138  0.037  2.399   3.9851e-02
   5_bss:   7.137  0.043  0.245 82.138  0.037  2.399   3.9851e-02
   5_xyz:   7.683  0.049  0.265 82.312  0.036  2.371   4.5536e-02
   5_adp:   7.683  0.049  0.265 82.312  0.036  2.371   4.5536e-02
   5_occ:   7.683  0.049  0.265 82.312  0.036  2.371   4.5536e-02
   5_bss:   7.683  0.049  0.265 82.312  0.036  2.371   4.5536e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  80.97   0.00  17.19  72.63   0.00  13.08  80.97   4.94  39.56
   1_occ:  80.97   0.00  17.19  72.63   0.00  13.08  80.97   4.94  39.56
   2_bss:  80.97   0.00  17.19  72.63   0.00  13.08  80.97   4.94  39.56
   2_xyz:  80.97   0.00  17.19  72.63   0.00  13.08  80.97   4.94  39.56
   2_adp:  81.23   1.04  16.92  73.38   1.04  12.73  81.23   5.48  39.74
   2_occ:  81.23   1.04  16.92  73.38   1.04  12.73  81.23   5.48  39.74
   3_bss:  81.23   1.04  16.92  73.38   1.04  12.73  81.23   5.48  39.74
   3_xyz:  81.23   1.04  16.92  73.38   1.04  12.73  81.23   5.48  39.74
   3_adp:  92.18   0.00  17.21  92.18   0.00  12.62  84.24   5.16  42.17
   3_occ:  92.18   0.00  17.21  92.18   0.00  12.62  84.24   5.16  42.17
   4_bss:  92.18   0.00  17.21  92.18   0.00  12.62  84.24   5.16  42.17
   4_xyz:  92.18   0.00  17.21  92.18   0.00  12.62  84.24   5.16  42.17
   4_adp:  93.01   0.00  16.96  93.01   0.00  12.40  84.71   5.17  41.81
   4_occ:  93.01   0.00  16.96  93.01   0.00  12.40  84.71   5.17  41.81
   5_bss:  93.01   0.00  16.96  93.01   0.00  12.40  84.71   5.17  41.81
   5_xyz:  93.01   0.00  16.96  93.01   0.00  12.40  84.71   5.17  41.81
   5_adp:  94.48   0.00  16.72  94.48   0.00  12.18  86.26   4.74  41.48
   5_occ:  94.48   0.00  16.72  94.48   0.00  12.18  86.26   4.74  41.48
   5_bss:  94.49   0.00  16.73  94.49   0.00  12.18  86.27   4.74  41.49
------------------------------------------------------------------------
 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:    1.418    0.019    0.285
   1_adp:    1.418    0.019    0.285
   1_occ:    1.418    0.019    0.285
   2_bss:    1.418    0.019    0.285
   2_xyz:    1.066    0.014    0.377
   2_adp:    1.066    0.014    0.377
   2_occ:    1.066    0.014    0.377
   3_bss:    1.066    0.014    0.377
   3_xyz:    1.007    0.066    0.425
   3_adp:    1.007    0.066    0.425
   3_occ:    1.007    0.066    0.425
   4_bss:    1.007    0.066    0.425
   4_xyz:    1.125    0.037    0.446
   4_adp:    1.125    0.037    0.446
   4_occ:    1.125    0.037    0.446
   5_bss:    1.125    0.037    0.446
   5_xyz:    1.225    0.076    0.460
   5_adp:    1.225    0.076    0.460
   5_occ:    1.225    0.076    0.460
   5_bss:    1.225    0.076    0.460
------------------------------------------------------------------------

CPU time actual refinement: 322.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/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_811/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_811/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.89 
  Macro-tasks:
    bulk solvent and scale       = 44.58  
    individual site refinement   = 130.07 
    weights calculation          = 28.37  
    collect and process          = 6.47   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 209.58 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 99.01  
    alpha_beta                      = 8.12   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 108.18 
    fmodel                         = 7.18   
    r_factors                      = 0.24   
    phase_errors                   = 11.11  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 237.01 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.567 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    632 calls, 98.69 s
gradients_fft:          577 calls, 94.79 s

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

# Date 2008-01-16 Time 05:42:41 PST -0800 (1200490961.91 s)
Start R-work = 0.3525, R-free = 0.3432 (no bulk solvent and anisotropic scale)
Final R-work = 0.1299, R-free = 0.1766 (no bulk solvent and anisotropic scale)

Start R-work = 0.3404, R-free = 0.3322
Final R-work = 0.1116, R-free = 0.1612