Starting phenix.real_space_refine
on Fri Aug 22 16:15:36 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x1i_37996/08_2025/8x1i_37996_trim.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      13      5.16       5
     C    1829      2.51       5
     N     484      2.21       5
     O     553      1.98       5
     H    2840      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5722
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 5694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 5694
          Classifications: {'peptide': 369}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 350}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.39, per 1000 atoms: 0.24
  Number of scatterers: 5722
  At special positions: 0
  Unit cell: (80.3, 55, 80.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      13     16.00
     P       2     15.00
     Mg      1     11.99
     O     553      8.00
     N     484      7.00
     C    1829      6.00
     H    2840      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 80.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  672

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 4 sheets defined
      43.9% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 44 through 48
      removed outlier: 4.161A  pdb=" N   GLY B  47 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 80 through 85
      removed outlier: 3.839A  pdb=" N   GLU B  84 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 80 through 85'
    Processing helix  chain 'B' and resid 102 through 117
      removed outlier: 3.520A  pdb=" N   THR B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   LEU B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 135
    Processing helix  chain 'B' and resid 138 through 146
      removed outlier: 3.525A  pdb=" N   TYR B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 177 through 186
      removed outlier: 3.652A  pdb=" N   PHE B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 198
    Processing helix  chain 'B' and resid 224 through 226
      No H-bonds generated for 'chain 'B' and resid 224 through 226'
    Processing helix  chain 'B' and resid 234 through 249
      removed outlier: 3.760A  pdb=" N   ALA B 238 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 272
      removed outlier: 3.926A  pdb=" N   LEU B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 308
      removed outlier: 4.138A  pdb=" N   SER B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 312
      removed outlier: 5.305A  pdb=" N   GLY B 312 " --> pdb=" O   PRO B 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 312'
    Processing helix  chain 'B' and resid 320 through 328
      removed outlier: 3.998A  pdb=" N   GLU B 325 " --> pdb=" O   GLY B 321 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET B 326 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 331
      No H-bonds generated for 'chain 'B' and resid 329 through 331'
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 344 through 357
    Processing helix  chain 'B' and resid 359 through 364
      removed outlier: 4.110A  pdb=" N   LYS B 364 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 30
      removed outlier: 6.226A  pdb=" N   LEU B   7 " --> pdb=" O   TYR B 125 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   GLY B 127 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B   9 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ALA B 122 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   ILE B 169 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   ILE B 124 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   SER B 171 " --> pdb=" O   ILE B 124 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LEU B 126 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   VAL B 173 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   THR B 128 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU B  62 " --> pdb=" O   MET B  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 221 through 222
    Processing sheet with id=AA3, first strand: chain 'B' and resid 221 through 222
      removed outlier: 7.506A  pdb=" N   TYR B 201 " --> pdb=" O   THR B 316 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   LEU B 318 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 203 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 277

    122 hydrogen bonds defined for protein.
    321 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.62 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.95 -     1.13: 2838
        1.13 -     1.30: 511
        1.30 -     1.47: 1102
        1.47 -     1.65: 1308
        1.65 -     1.82: 24
  Bond restraints: 5783
  Sorted by residual:
  bond pdb=" N   ILE B 352 "
       pdb=" H   ILE B 352 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CD2 TYR B  93 "
       pdb=" HD2 TYR B  93 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   GLU B  90 "
       pdb=" H   GLU B  90 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   THR B 128 "
       pdb=" H   THR B 128 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   ALA B 137 "
       pdb=" H   ALA B 137 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 5778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.38: 9906
        4.38 -     8.76: 555
        8.76 -    13.14: 11
       13.14 -    17.52: 0
       17.52 -    21.90: 1
  Bond angle restraints: 10473
  Sorted by residual:
  angle pdb=" N   PRO B 225 "
        pdb=" CA  PRO B 225 "
        pdb=" C   PRO B 225 "
      ideal   model   delta    sigma   weight residual
     110.70  120.21   -9.51 1.22e+00 6.72e-01 6.08e+01
  angle pdb=" O1B ADP B 401 "
        pdb=" PB  ADP B 401 "
        pdb=" O2B ADP B 401 "
      ideal   model   delta    sigma   weight residual
     119.90   98.00   21.90 3.00e+00 1.11e-01 5.33e+01
  angle pdb=" CB  HIS B 253 "
        pdb=" CG  HIS B 253 "
        pdb=" CD2 HIS B 253 "
      ideal   model   delta    sigma   weight residual
     131.20  124.62    6.58 1.30e+00 5.92e-01 2.56e+01
  angle pdb=" C   ASN B 341 "
        pdb=" N   PRO B 342 "
        pdb=" CA  PRO B 342 "
      ideal   model   delta    sigma   weight residual
     119.05  124.59   -5.54 1.11e+00 8.12e-01 2.49e+01
  angle pdb=" C   ILE B 168 "
        pdb=" N   ILE B 169 "
        pdb=" CA  ILE B 169 "
      ideal   model   delta    sigma   weight residual
     120.70  126.81   -6.11 1.25e+00 6.40e-01 2.39e+01
  ... (remaining 10468 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.15: 2544
       27.15 -    54.31: 116
       54.31 -    81.46: 55
       81.46 -   108.61: 1
      108.61 -   135.77: 2
  Dihedral angle restraints: 2718
    sinusoidal: 1491
      harmonic: 1227
  Sorted by residual:
  dihedral pdb=" O2A ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" PB  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   75.77 -135.77     1      2.00e+01 2.50e-03 4.12e+01
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  164.84  135.16     1      2.00e+01 2.50e-03 4.10e+01
  dihedral pdb=" CA  ASP B  12 "
           pdb=" C   ASP B  12 "
           pdb=" N   PRO B  13 "
           pdb=" CA  PRO B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.06   28.94     0      5.00e+00 4.00e-02 3.35e+01
  ... (remaining 2715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.091: 292
       0.091 -    0.182: 121
       0.182 -    0.273: 26
       0.273 -    0.364: 4
       0.364 -    0.454: 1
  Chirality restraints: 444
  Sorted by residual:
  chirality pdb=" CA  PRO B 225 "
            pdb=" N   PRO B 225 "
            pdb=" C   PRO B 225 "
            pdb=" CB  PRO B 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.26    0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" CA  LEU B 357 "
            pdb=" N   LEU B 357 "
            pdb=" C   LEU B 357 "
            pdb=" CB  LEU B 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CA  ASP B  12 "
            pdb=" N   ASP B  12 "
            pdb=" C   ASP B  12 "
            pdb=" CB  ASP B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  ... (remaining 441 not shown)

  Planarity restraints: 866
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ADP B 401 "   -0.313 2.00e-02 2.50e+03   1.27e-01 4.44e+02
        pdb=" C2  ADP B 401 "    0.058 2.00e-02 2.50e+03
        pdb=" C4  ADP B 401 "    0.085 2.00e-02 2.50e+03
        pdb=" C5  ADP B 401 "    0.034 2.00e-02 2.50e+03
        pdb=" C6  ADP B 401 "   -0.048 2.00e-02 2.50e+03
        pdb=" C8  ADP B 401 "    0.115 2.00e-02 2.50e+03
        pdb=" N1  ADP B 401 "   -0.031 2.00e-02 2.50e+03
        pdb=" N3  ADP B 401 "    0.103 2.00e-02 2.50e+03
        pdb=" N6  ADP B 401 "   -0.165 2.00e-02 2.50e+03
        pdb=" N7  ADP B 401 "    0.064 2.00e-02 2.50e+03
        pdb=" N9  ADP B 401 "    0.097 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  95 "   -0.198 2.00e-02 2.50e+03   7.98e-02 2.55e+02
        pdb=" CG  TRP B  95 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  95 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  95 "    0.050 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  95 "    0.085 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  95 "    0.024 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  95 "    0.078 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  95 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  95 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  95 "   -0.047 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  95 "   -0.023 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  95 "    0.107 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  95 "    0.109 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  95 "   -0.082 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  95 "    0.028 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  95 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 210 "   -0.293 9.50e-02 1.11e+02   1.38e-01 2.26e+02
        pdb=" NE  ARG B 210 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 210 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 210 "   -0.106 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 210 "   -0.021 2.00e-02 2.50e+03
        pdb="HH11 ARG B 210 "    0.207 2.00e-02 2.50e+03
        pdb="HH12 ARG B 210 "   -0.043 2.00e-02 2.50e+03
        pdb="HH21 ARG B 210 "    0.141 2.00e-02 2.50e+03
        pdb="HH22 ARG B 210 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 863 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 467
        2.22 -     2.81: 10970
        2.81 -     3.41: 16009
        3.41 -     4.00: 20764
        4.00 -     4.60: 30904
  Nonbonded interactions: 79114
  Sorted by model distance:
  nonbonded pdb=" HG  SER B  81 "
            pdb=" OE2 GLU B  84 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" OD1 ASP B  98 "
            pdb=" HG  SER B 100 "
     model   vdw
     1.635 2.450
  nonbonded pdb=" OD1 ASP B 213 "
            pdb=" HG  SER B 230 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" HG1 THR B  25 "
            pdb=" OE2 GLU B  56 "
     model   vdw
     1.638 2.450
  nonbonded pdb=" OE1 GLU B 263 "
            pdb=" HH  TYR B 275 "
     model   vdw
     1.644 2.450
  ... (remaining 79109 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.430
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.142   2943  Z= 0.724
  Angle     :  1.871  21.904   3994  Z= 1.188
  Chirality :  0.102   0.454    444
  Planarity :  0.014   0.127    516
  Dihedral  : 15.720 135.766   1083
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  :  4.56 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.39), residues: 367
  helix: -1.86 (0.40), residues: 106
  sheet: -0.06 (0.63), residues: 60
  loop : -1.46 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 301 
 TYR   0.102   0.018   TYR B 275 
 PHE   0.080   0.015   PHE B 268 
 TRP   0.125   0.029   TRP B  95 
 HIS   0.011   0.004   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.01239 ( 2943)
  covalent geometry    : angle       1.87101 ( 3994)
  hydrogen bonds       : bond        0.15410 (  120)
  hydrogen bonds       : angle       7.89890 (  321)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1673
  time to fit residues: 14.2567
Evaluate side-chains
  56 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  338 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.088445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.075596 restraints weight = 24639.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.078835 restraints weight = 10655.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.080985 restraints weight = 5828.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082422 restraints weight = 3775.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.083316 restraints weight = 2739.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2943  Z= 0.162
  Angle     :  0.779   7.231   3994  Z= 0.409
  Chirality :  0.048   0.169    444
  Planarity :  0.005   0.052    516
  Dihedral  : 12.924 107.005    414
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 10.10 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.41), residues: 367
  helix: -0.39 (0.47), residues: 119
  sheet: -0.22 (0.59), residues: 70
  loop : -1.67 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 172 
 TYR   0.012   0.002   TYR B 239 
 PHE   0.015   0.002   PHE B 328 
 TRP   0.005   0.001   TRP B 277 
 HIS   0.002   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 2943)
  covalent geometry    : angle       0.77873 ( 3994)
  hydrogen bonds       : bond        0.04487 (  120)
  hydrogen bonds       : angle       5.87771 (  321)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7419 (mt-10)
REVERT: B  275 TYR cc_start: 0.8665 (t80) cc_final: 0.8392 (t80)
REVERT: B  323 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8064 (t)
  outliers start: 9
  outliers final: 4
  residues processed: 55
  average time/residue: 0.2018
  time to fit residues: 12.6276
Evaluate side-chains
  40 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  338 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 341 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.091536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.078385 restraints weight = 25456.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.081681 restraints weight = 10780.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.083783 restraints weight = 6018.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.085213 restraints weight = 4014.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.086153 restraints weight = 2998.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2943  Z= 0.182
  Angle     :  0.696   7.506   3994  Z= 0.357
  Chirality :  0.046   0.167    444
  Planarity :  0.004   0.045    516
  Dihedral  : 11.508  92.816    410
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.70 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.43), residues: 367
  helix:  0.27 (0.50), residues: 119
  sheet: -0.24 (0.62), residues: 70
  loop : -1.53 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 351 
 TYR   0.010   0.002   TYR B 189 
 PHE   0.011   0.001   PHE B 328 
 TRP   0.007   0.001   TRP B 277 
 HIS   0.002   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2943)
  covalent geometry    : angle       0.69629 ( 3994)
  hydrogen bonds       : bond        0.03785 (  120)
  hydrogen bonds       : angle       5.50984 (  321)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  323 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8309 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1214
  time to fit residues: 5.9940
Evaluate side-chains
  37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
B 366 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.092681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.079291 restraints weight = 25218.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082659 restraints weight = 10736.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.084805 restraints weight = 6013.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.086218 restraints weight = 4016.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.087163 restraints weight = 3011.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2943  Z= 0.122
  Angle     :  0.644   7.176   3994  Z= 0.320
  Chirality :  0.045   0.176    444
  Planarity :  0.004   0.048    516
  Dihedral  :  9.969  79.441    410
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.36 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.44), residues: 367
  helix:  0.68 (0.52), residues: 115
  sheet: -0.45 (0.59), residues: 72
  loop : -1.24 (0.46), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.006   0.001   TYR B  93 
 PHE   0.008   0.001   PHE B 159 
 TRP   0.002   0.001   TRP B  95 
 HIS   0.001   0.000   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 2943)
  covalent geometry    : angle       0.64366 ( 3994)
  hydrogen bonds       : bond        0.03229 (  120)
  hydrogen bonds       : angle       5.13543 (  321)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  291 MET cc_start: 0.8947 (tpp) cc_final: 0.8621 (tpp)
  outliers start: 6
  outliers final: 5
  residues processed: 42
  average time/residue: 0.1412
  time to fit residues: 7.2523
Evaluate side-chains
  38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  338 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    0.0470
   chunk 8 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8082

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.092312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.078971 restraints weight = 25580.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.082337 restraints weight = 10675.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.084562 restraints weight = 5881.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.085959 restraints weight = 3873.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086820 restraints weight = 2873.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2943  Z= 0.114
  Angle     :  0.617   6.813   3994  Z= 0.305
  Chirality :  0.044   0.152    444
  Planarity :  0.004   0.048    516
  Dihedral  :  9.407  71.807    409
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.05 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.45), residues: 367
  helix:  0.57 (0.51), residues: 121
  sheet: -0.36 (0.59), residues: 74
  loop : -1.21 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.006   0.001   TYR B 125 
 PHE   0.010   0.001   PHE B 268 
 TRP   0.002   0.001   TRP B  95 
 HIS   0.001   0.000   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2943)
  covalent geometry    : angle       0.61671 ( 3994)
  hydrogen bonds       : bond        0.03215 (  120)
  hydrogen bonds       : angle       5.05875 (  321)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.1413
  time to fit residues: 6.0847
Evaluate side-chains
  35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    0.0870
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.092951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.079914 restraints weight = 24914.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.083263 restraints weight = 10428.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.085417 restraints weight = 5712.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.086828 restraints weight = 3730.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.087743 restraints weight = 2738.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.5555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2943  Z= 0.106
  Angle     :  0.607   6.256   3994  Z= 0.296
  Chirality :  0.044   0.151    444
  Planarity :  0.004   0.048    516
  Dihedral  :  8.969  65.830    409
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.36 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.46), residues: 367
  helix:  0.78 (0.52), residues: 116
  sheet: -0.40 (0.59), residues: 74
  loop : -1.02 (0.49), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 172 
 TYR   0.006   0.001   TYR B  77 
 PHE   0.017   0.001   PHE B 268 
 TRP   0.002   0.001   TRP B 150 
 HIS   0.001   0.000   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2943)
  covalent geometry    : angle       0.60728 ( 3994)
  hydrogen bonds       : bond        0.03051 (  120)
  hydrogen bonds       : angle       4.96525 (  321)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  291 MET cc_start: 0.8878 (tpp) cc_final: 0.8528 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 33
  average time/residue: 0.1117
  time to fit residues: 4.6185
Evaluate side-chains
  32 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.092429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.079111 restraints weight = 25359.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.082503 restraints weight = 10732.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.084642 restraints weight = 5948.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.085820 restraints weight = 3945.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086831 restraints weight = 3045.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.5731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2943  Z= 0.116
  Angle     :  0.608   6.121   3994  Z= 0.295
  Chirality :  0.044   0.149    444
  Planarity :  0.004   0.046    516
  Dihedral  :  8.724  61.896    409
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.70 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.46), residues: 367
  helix:  0.90 (0.52), residues: 117
  sheet: -0.39 (0.59), residues: 74
  loop : -0.94 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 172 
 TYR   0.006   0.001   TYR B 135 
 PHE   0.013   0.001   PHE B 268 
 TRP   0.003   0.001   TRP B  95 
 HIS   0.001   0.000   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 2943)
  covalent geometry    : angle       0.60792 ( 3994)
  hydrogen bonds       : bond        0.03007 (  120)
  hydrogen bonds       : angle       4.89284 (  321)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6702 (m170)
REVERT: B  291 MET cc_start: 0.8944 (tpp) cc_final: 0.8538 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1260
  time to fit residues: 5.7615
Evaluate side-chains
  36 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.092747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.079379 restraints weight = 24993.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.082716 restraints weight = 10580.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.084844 restraints weight = 5884.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.086199 restraints weight = 3905.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.087142 restraints weight = 2947.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2943  Z= 0.105
  Angle     :  0.599   5.718   3994  Z= 0.289
  Chirality :  0.044   0.149    444
  Planarity :  0.004   0.047    516
  Dihedral  :  8.547  57.735    409
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.36 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.47), residues: 367
  helix:  1.14 (0.53), residues: 117
  sheet: -0.50 (0.56), residues: 80
  loop : -0.69 (0.54), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 172 
 TYR   0.007   0.001   TYR B 275 
 PHE   0.013   0.001   PHE B 268 
 TRP   0.002   0.001   TRP B  95 
 HIS   0.005   0.001   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 2943)
  covalent geometry    : angle       0.59926 ( 3994)
  hydrogen bonds       : bond        0.02809 (  120)
  hydrogen bonds       : angle       4.84715 (  321)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  291 MET cc_start: 0.8921 (tpp) cc_final: 0.8549 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1203
  time to fit residues: 5.4955
Evaluate side-chains
  33 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  338 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.092729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.079221 restraints weight = 25164.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.082606 restraints weight = 10732.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.084772 restraints weight = 5980.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.086160 restraints weight = 3975.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086968 restraints weight = 2975.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.6075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2943  Z= 0.103
  Angle     :  0.603   5.766   3994  Z= 0.289
  Chirality :  0.044   0.142    444
  Planarity :  0.004   0.047    516
  Dihedral  :  8.261  57.622    409
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.36 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.47), residues: 367
  helix:  1.19 (0.53), residues: 118
  sheet: -0.43 (0.56), residues: 79
  loop : -0.83 (0.52), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.013   0.001   TYR B 134 
 PHE   0.011   0.001   PHE B 268 
 TRP   0.003   0.001   TRP B  95 
 HIS   0.002   0.001   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2943)
  covalent geometry    : angle       0.60343 ( 3994)
  hydrogen bonds       : bond        0.02754 (  120)
  hydrogen bonds       : angle       4.79649 (  321)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  291 MET cc_start: 0.8938 (tpp) cc_final: 0.8542 (tpp)
REVERT: B  298 ASP cc_start: 0.7727 (m-30) cc_final: 0.7209 (m-30)
REVERT: B  302 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7403 (mm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 32
  average time/residue: 0.1316
  time to fit residues: 5.1646
Evaluate side-chains
  35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.092474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.079011 restraints weight = 25318.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.082399 restraints weight = 10791.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.084587 restraints weight = 5949.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.085990 restraints weight = 3916.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086884 restraints weight = 2917.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.6159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2943  Z= 0.104
  Angle     :  0.600   6.930   3994  Z= 0.287
  Chirality :  0.043   0.141    444
  Planarity :  0.004   0.047    516
  Dihedral  :  8.119  57.671    409
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.36 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.47), residues: 367
  helix:  1.24 (0.53), residues: 118
  sheet: -0.28 (0.57), residues: 76
  loop : -0.90 (0.51), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.009   0.001   TYR B 134 
 PHE   0.010   0.001   PHE B 268 
 TRP   0.002   0.000   TRP B  95 
 HIS   0.001   0.000   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 2943)
  covalent geometry    : angle       0.60016 ( 3994)
  hydrogen bonds       : bond        0.02689 (  120)
  hydrogen bonds       : angle       4.78297 (  321)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  734 Ramachandran restraints generated.
    367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  291 MET cc_start: 0.8938 (tpp) cc_final: 0.8595 (tpp)
REVERT: B  298 ASP cc_start: 0.7759 (m-30) cc_final: 0.7223 (m-30)
REVERT: B  302 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7436 (mm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 31
  average time/residue: 0.1356
  time to fit residues: 5.3243
Evaluate side-chains
  34 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.091436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.077893 restraints weight = 24938.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.081250 restraints weight = 10715.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.083409 restraints weight = 6005.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.084767 restraints weight = 4006.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.085676 restraints weight = 3012.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.6280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2943  Z= 0.134
  Angle     :  0.613   6.524   3994  Z= 0.295
  Chirality :  0.043   0.142    444
  Planarity :  0.004   0.046    516
  Dihedral  :  8.050  59.187    409
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.68 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.47), residues: 367
  helix:  1.18 (0.53), residues: 118
  sheet: -0.29 (0.57), residues: 76
  loop : -0.94 (0.51), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 172 
 TYR   0.010   0.002   TYR B 135 
 PHE   0.009   0.001   PHE B 268 
 TRP   0.005   0.001   TRP B 150 
 HIS   0.001   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2943)
  covalent geometry    : angle       0.61274 ( 3994)
  hydrogen bonds       : bond        0.02762 (  120)
  hydrogen bonds       : angle       4.77875 (  321)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1451.29 seconds
wall clock time: 25 minutes 17.33 seconds (1517.33 seconds total)