Starting phenix.real_space_refine
on Tue Mar  3 11:57:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lv4_63412/03_2026/9lv4_63412.map"
  }
  resolution = 2.67
  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=  -0.002 sd=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    2242      2.51       5
     N     615      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3549
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2877
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 24, 'TRANS': 343}
          Chain breaks: 10
    Chain: "A"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 672
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 2, 'TRANS': 80}
  Time building chain proxies: 0.88, per 1000 atoms: 0.25
  Number of scatterers: 3549
  At special positions: 0
  Unit cell: (64.152, 68.04, 108.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O     656      8.00
     N     615      7.00
     C    2242      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  44 " - pdb=" SG  CYS B 102 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 211 " - pdb=" SG  CYS B 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 233 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 227 " - pdb=" SG  CYS B 240 " distance=2.18
    Simple disulfide: pdb=" SG  CYS B 242 " - pdb=" SG  CYS B 251 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 255 " - pdb=" SG  CYS B 264 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 268 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 289 " - pdb=" SG  CYS B 298 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 424 " distance=2.12

  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: 0.19
  Conformation dependent library (CDL) restraints added in 131.7 milliseconds
  

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  840

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 10 sheets defined
      19.1% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 182 through 186
    Processing helix  chain 'B' and resid 295 through 299
      removed outlier: 4.242A  pdb=" N   ASN B 299 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 312
    Processing helix  chain 'B' and resid 379 through 381
      No H-bonds generated for 'chain 'B' and resid 379 through 381'
    Processing helix  chain 'A' and resid 9 through 27
      removed outlier: 3.510A  pdb=" N   GLU A  13 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ILE A  15 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LEU A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 4.994A  pdb=" N   TYR A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   GLU A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS A  49 " --> pdb=" O   GLU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 67
      removed outlier: 4.431A  pdb=" N   ASP A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 90
      removed outlier: 3.782A  pdb=" N   LEU A  84 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 74 through 75
    Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 59
    Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133
      removed outlier: 3.519A  pdb=" N   VAL B 133 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 144
    Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 165
      removed outlier: 5.204A  pdb=" N   PHE B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   LYS B 157 " --> pdb=" O   PHE B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 233
    Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 247
    Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 372
      removed outlier: 3.506A  pdb=" N   VAL B 406 " --> pdb=" O   ASN B 399 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 383 through 384

    114 hydrogen bonds defined for protein.
    285 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: 0.37

  Time building geometry restraints manager: 0.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1157
        1.35 -     1.47: 802
        1.47 -     1.59: 1612
        1.59 -     1.71: 0
        1.71 -     1.83: 49
  Bond restraints: 3620
  Sorted by residual:
  bond pdb=" CA  LYS A  70 "
       pdb=" C   LYS A  70 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.72e-02 3.38e+03 5.60e+00
  bond pdb=" CB  ARG B 114 "
       pdb=" CG  ARG B 114 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.16e+00
  bond pdb=" CG  MET B 118 "
       pdb=" SD  MET B 118 "
    ideal  model  delta    sigma   weight residual
    1.803  1.759  0.044 2.50e-02 1.60e+03 3.10e+00
  bond pdb=" CB  ILE B 113 "
       pdb=" CG2 ILE B 113 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.71e+00
  bond pdb=" C   CYS B 287 "
       pdb=" N   SER B 288 "
    ideal  model  delta    sigma   weight residual
    1.328  1.313  0.015 1.04e-02 9.25e+03 2.13e+00
  ... (remaining 3615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 4775
        2.52 -     5.05: 82
        5.05 -     7.57: 9
        7.57 -    10.09: 1
       10.09 -    12.62: 2
  Bond angle restraints: 4869
  Sorted by residual:
  angle pdb=" CA  GLY B 261 "
        pdb=" C   GLY B 261 "
        pdb=" O   GLY B 261 "
      ideal   model   delta    sigma   weight residual
     122.22  119.73    2.49 6.50e-01 2.37e+00 1.47e+01
  angle pdb=" CB  MET B 118 "
        pdb=" CG  MET B 118 "
        pdb=" SD  MET B 118 "
      ideal   model   delta    sigma   weight residual
     112.70  124.09  -11.39 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" CG  MET B 118 "
        pdb=" SD  MET B 118 "
        pdb=" CE  MET B 118 "
      ideal   model   delta    sigma   weight residual
     100.90   92.77    8.13 2.20e+00 2.07e-01 1.37e+01
  angle pdb=" N   ASP B 283 "
        pdb=" CA  ASP B 283 "
        pdb=" C   ASP B 283 "
      ideal   model   delta    sigma   weight residual
     113.57  118.17   -4.60 1.38e+00 5.25e-01 1.11e+01
  angle pdb=" CA  MET B 118 "
        pdb=" CB  MET B 118 "
        pdb=" CG  MET B 118 "
      ideal   model   delta    sigma   weight residual
     114.10  107.59    6.51 2.00e+00 2.50e-01 1.06e+01
  ... (remaining 4864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 1974
       17.26 -    34.52: 214
       34.52 -    51.77: 33
       51.77 -    69.03: 9
       69.03 -    86.29: 5
  Dihedral angle restraints: 2235
    sinusoidal: 946
      harmonic: 1289
  Sorted by residual:
  dihedral pdb=" CB  CYS B 370 "
           pdb=" SG  CYS B 370 "
           pdb=" SG  CYS B 424 "
           pdb=" CB  CYS B 424 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.34   53.34     1      1.00e+01 1.00e-02 3.87e+01
  dihedral pdb=" CB  CYS B 224 "
           pdb=" SG  CYS B 224 "
           pdb=" SG  CYS B 233 "
           pdb=" CB  CYS B 233 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.77   52.23     1      1.00e+01 1.00e-02 3.72e+01
  dihedral pdb=" CA  GLU B 256 "
           pdb=" C   GLU B 256 "
           pdb=" N   LEU B 257 "
           pdb=" CA  LEU B 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.67  -28.33     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 2232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 342
       0.045 -    0.089: 134
       0.089 -    0.133: 45
       0.133 -    0.178: 6
       0.178 -    0.222: 2
  Chirality restraints: 529
  Sorted by residual:
  chirality pdb=" CA  ASP B 283 "
            pdb=" N   ASP B 283 "
            pdb=" C   ASP B 283 "
            pdb=" CB  ASP B 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL B 139 "
            pdb=" CA  VAL B 139 "
            pdb=" CG1 VAL B 139 "
            pdb=" CG2 VAL B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 526 not shown)

  Planarity restraints: 623
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 281 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.56e+00
        pdb=" N   PRO B 282 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 282 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 282 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  40 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   TYR A  40 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR A  40 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  41 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  35 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A  36 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A  36 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  36 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 620 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 63
        2.65 -     3.21: 3411
        3.21 -     3.77: 5591
        3.77 -     4.34: 7661
        4.34 -     4.90: 12160
  Nonbonded interactions: 28886
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  60 "
            pdb=" CD  ARG B 114 "
     model   vdw
     2.086 3.440
  nonbonded pdb=" ND2 ASN B 229 "
            pdb=" O   CYS B 251 "
     model   vdw
     2.099 3.120
  nonbonded pdb=" O   ALA A  58 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   SER B 269 "
            pdb=" OH  TYR B 277 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NE2 GLN B  67 "
            pdb=" O   ASN B  97 "
     model   vdw
     2.244 3.120
  ... (remaining 28881 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             5.410
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.100
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:9.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5450
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      :  0.007   0.149   3631  Z= 0.314
  Angle     :  0.913  12.773   4891  Z= 0.504
  Chirality :  0.053   0.222    529
  Planarity :  0.005   0.047    623
  Dihedral  : 14.405  86.288   1362
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 27.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  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 are not related in a simple way.
  whole: -5.11 (0.31), residues: 427
  helix: -3.92 (0.39), residues: 64
  sheet: -2.53 (0.44), residues: 112
  loop : -3.84 (0.29), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 119 
 TYR   0.018   0.003   TYR B 156 
 PHE   0.023   0.002   PHE B 101 
 TRP   0.014   0.002   TRP B 293 
 HIS   0.004   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 3620)
  covalent geometry    : angle       0.88110 ( 4869)
  SS BOND              : bond        0.05253 (   11)
  SS BOND              : angle       3.69744 (   22)
  hydrogen bonds       : bond        0.16476 (  114)
  hydrogen bonds       : angle       8.33717 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.6011
  time to fit residues: 58.0417
Evaluate side-chains
  52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B  30 ASN
B  52 HIS
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 ASN
B 230 ASN
** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
B 438 ASN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  62 HIS
A  63 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.189215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.165159 restraints weight = 6496.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.4641 rms_B_bonded: 4.22
r_work: 0.4493 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.4493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5786
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3631  Z= 0.175
  Angle     :  0.770   8.953   4891  Z= 0.396
  Chirality :  0.048   0.165    529
  Planarity :  0.005   0.044    623
  Dihedral  :  6.106  22.143    469
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.79 %
    Favored  : 73.59 %
  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 are not related in a simple way.
  whole: -3.97 (0.35), residues: 427
  helix: -3.36 (0.42), residues: 69
  sheet: -2.06 (0.45), residues: 111
  loop : -2.77 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 267 
 TYR   0.014   0.001   TYR B 156 
 PHE   0.014   0.002   PHE B 101 
 TRP   0.014   0.002   TRP B 375 
 HIS   0.007   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3620)
  covalent geometry    : angle       0.76430 ( 4869)
  SS BOND              : bond        0.00745 (   11)
  SS BOND              : angle       1.60063 (   22)
  hydrogen bonds       : bond        0.04222 (  114)
  hydrogen bonds       : angle       6.59902 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  212 GLU cc_start: 0.8461 (tt0) cc_final: 0.8001 (pm20)
REVERT: B  236 ASP cc_start: 0.6818 (t70) cc_final: 0.6504 (m-30)
REVERT: B  432 MET cc_start: 0.2810 (OUTLIER) cc_final: 0.2534 (tmm)
  outliers start: 18
  outliers final: 9
  residues processed: 68
  average time/residue: 0.4805
  time to fit residues: 33.7845
Evaluate side-chains
  55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 CYS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  432 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   8 GLN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.186396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.161831 restraints weight = 6420.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.4610 rms_B_bonded: 4.27
r_work: 0.4465 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5864
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3631  Z= 0.185
  Angle     :  0.760   7.948   4891  Z= 0.393
  Chirality :  0.048   0.222    529
  Planarity :  0.005   0.048    623
  Dihedral  :  5.922  27.314    469
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 23.08 %
    Favored  : 72.56 %
  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 are not related in a simple way.
  whole: -3.36 (0.37), residues: 427
  helix: -3.03 (0.46), residues: 71
  sheet: -1.52 (0.49), residues: 107
  loop : -2.36 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 205 
 TYR   0.015   0.002   TYR B 156 
 PHE   0.018   0.002   PHE B 101 
 TRP   0.011   0.001   TRP B 375 
 HIS   0.004   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3620)
  covalent geometry    : angle       0.75094 ( 4869)
  SS BOND              : bond        0.00612 (   11)
  SS BOND              : angle       1.86116 (   22)
  hydrogen bonds       : bond        0.03919 (  114)
  hydrogen bonds       : angle       6.40226 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.4527 (mt)
REVERT: A   43 MET cc_start: 0.4593 (mpm) cc_final: 0.3849 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 71
  average time/residue: 0.4159
  time to fit residues: 30.7113
Evaluate side-chains
  60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 CYS
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 358 HIS
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.184181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.159406 restraints weight = 6458.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4576 rms_B_bonded: 4.27
r_work: 0.4433 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.4433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5916
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3631  Z= 0.211
  Angle     :  0.784   8.055   4891  Z= 0.407
  Chirality :  0.050   0.229    529
  Planarity :  0.006   0.048    623
  Dihedral  :  6.059  29.761    469
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 22.82 %
    Favored  : 69.74 %
  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 are not related in a simple way.
  whole: -3.13 (0.37), residues: 427
  helix: -2.53 (0.50), residues: 71
  sheet: -1.34 (0.50), residues: 109
  loop : -2.35 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 205 
 TYR   0.016   0.002   TYR B 156 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.015   0.001   TRP B 375 
 HIS   0.008   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 3620)
  covalent geometry    : angle       0.77504 ( 4869)
  SS BOND              : bond        0.00679 (   11)
  SS BOND              : angle       1.95154 (   22)
  hydrogen bonds       : bond        0.04014 (  114)
  hydrogen bonds       : angle       6.39503 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 52
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  206 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6635 (tp)
REVERT: B  210 ARG cc_start: 0.7923 (tmm160) cc_final: 0.7469 (tmm160)
REVERT: B  219 GLU cc_start: 0.7499 (mp0) cc_final: 0.7232 (mp0)
REVERT: B  228 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8400 (mtt)
REVERT: B  236 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6973 (m-30)
REVERT: A   43 MET cc_start: 0.4754 (mpm) cc_final: 0.3575 (tpp)
  outliers start: 29
  outliers final: 14
  residues processed: 69
  average time/residue: 0.4274
  time to fit residues: 30.6944
Evaluate side-chains
  62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 CYS
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  236 ASP
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 ASN
A   8 GLN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.183994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.159076 restraints weight = 6442.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.4573 rms_B_bonded: 4.25
r_work: 0.4431 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5923
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3631  Z= 0.189
  Angle     :  0.753   8.126   4891  Z= 0.392
  Chirality :  0.048   0.159    529
  Planarity :  0.005   0.048    623
  Dihedral  :  5.929  28.810    469
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 26.92 %
    Favored  : 66.67 %
  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 are not related in a simple way.
  whole: -2.74 (0.38), residues: 427
  helix: -1.98 (0.54), residues: 72
  sheet: -1.15 (0.51), residues: 109
  loop : -2.14 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.018   0.003   TYR A  40 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.012   0.001   TRP B 375 
 HIS   0.009   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3620)
  covalent geometry    : angle       0.74403 ( 4869)
  SS BOND              : bond        0.00656 (   11)
  SS BOND              : angle       1.91412 (   22)
  hydrogen bonds       : bond        0.03815 (  114)
  hydrogen bonds       : angle       6.27248 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 53
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  206 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6352 (tp)
REVERT: B  210 ARG cc_start: 0.7947 (tmm160) cc_final: 0.7473 (tmm160)
REVERT: B  219 GLU cc_start: 0.7517 (mp0) cc_final: 0.7288 (mp0)
REVERT: B  228 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8357 (mtt)
REVERT: A   43 MET cc_start: 0.4841 (mpm) cc_final: 0.3786 (tpp)
  outliers start: 25
  outliers final: 15
  residues processed: 71
  average time/residue: 0.4560
  time to fit residues: 33.6344
Evaluate side-chains
  64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 CYS
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 43 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 ASN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.187942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.163569 restraints weight = 6456.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4631 rms_B_bonded: 4.28
r_work: 0.4488 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5834
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3631  Z= 0.140
  Angle     :  0.713   7.881   4891  Z= 0.369
  Chirality :  0.046   0.176    529
  Planarity :  0.005   0.052    623
  Dihedral  :  5.611  25.701    469
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 27.69 %
    Favored  : 66.67 %
  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 are not related in a simple way.
  whole: -2.39 (0.39), residues: 427
  helix: -1.76 (0.54), residues: 71
  sheet: -1.02 (0.52), residues: 109
  loop : -1.82 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.013   0.002   TYR B 156 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 375 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3620)
  covalent geometry    : angle       0.70535 ( 4869)
  SS BOND              : bond        0.00504 (   11)
  SS BOND              : angle       1.67389 (   22)
  hydrogen bonds       : bond        0.03463 (  114)
  hydrogen bonds       : angle       5.98619 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 50
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7056 (t)
REVERT: B  111 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.4732 (mt)
REVERT: B  206 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6242 (tp)
REVERT: B  210 ARG cc_start: 0.7805 (tmm160) cc_final: 0.7356 (tmm160)
REVERT: B  219 GLU cc_start: 0.7427 (mp0) cc_final: 0.7192 (mp0)
REVERT: B  228 MET cc_start: 0.8698 (mtt) cc_final: 0.8330 (mtp)
REVERT: B  236 ASP cc_start: 0.6719 (m-30) cc_final: 0.6440 (p0)
REVERT: B  247 MET cc_start: 0.6150 (ttm) cc_final: 0.5760 (tpt)
REVERT: A   43 MET cc_start: 0.4918 (mpm) cc_final: 0.3925 (tpp)
  outliers start: 22
  outliers final: 13
  residues processed: 66
  average time/residue: 0.4479
  time to fit residues: 30.7187
Evaluate side-chains
  61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 GLN ** 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 = 0.4931 r_free = 0.4931 target = 0.188198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.163527 restraints weight = 6582.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4632 rms_B_bonded: 4.34
r_work: 0.4490 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5846
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3631  Z= 0.146
  Angle     :  0.725   7.866   4891  Z= 0.373
  Chirality :  0.046   0.149    529
  Planarity :  0.005   0.054    623
  Dihedral  :  5.612  24.952    469
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 27.95 %
    Favored  : 66.41 %
  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 are not related in a simple way.
  whole: -2.17 (0.40), residues: 427
  helix: -1.77 (0.55), residues: 71
  sheet: -0.85 (0.54), residues: 100
  loop : -1.61 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.016   0.002   TYR B 156 
 PHE   0.009   0.001   PHE B 101 
 TRP   0.009   0.001   TRP B 375 
 HIS   0.002   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3620)
  covalent geometry    : angle       0.71541 ( 4869)
  SS BOND              : bond        0.00535 (   11)
  SS BOND              : angle       1.92761 (   22)
  hydrogen bonds       : bond        0.03458 (  114)
  hydrogen bonds       : angle       5.93288 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 50
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7043 (t)
REVERT: B  111 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.4740 (mt)
REVERT: B  206 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6254 (tp)
REVERT: B  210 ARG cc_start: 0.7830 (tmm160) cc_final: 0.7362 (tmm160)
REVERT: B  219 GLU cc_start: 0.7493 (mp0) cc_final: 0.7267 (mp0)
REVERT: B  228 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8362 (mtp)
REVERT: B  234 HIS cc_start: 0.7565 (t70) cc_final: 0.7217 (t-90)
REVERT: B  247 MET cc_start: 0.6151 (ttm) cc_final: 0.5794 (tpt)
REVERT: B  379 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7896 (p)
REVERT: A   43 MET cc_start: 0.5158 (mpm) cc_final: 0.4269 (tpp)
  outliers start: 22
  outliers final: 12
  residues processed: 67
  average time/residue: 0.3552
  time to fit residues: 24.8943
Evaluate side-chains
  64 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain A residue   19 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0980
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  30 ASN
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4960 r_free = 0.4960 target = 0.188393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.165911 restraints weight = 6663.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4684 rms_B_bonded: 4.12
r_work: 0.4536 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5895
moved from start:          0.5806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3631  Z= 0.138
  Angle     :  0.714   8.628   4891  Z= 0.366
  Chirality :  0.047   0.255    529
  Planarity :  0.005   0.054    623
  Dihedral  :  5.378  25.048    469
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 28.46 %
    Favored  : 66.67 %
  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 are not related in a simple way.
  whole: -2.00 (0.40), residues: 427
  helix: -1.67 (0.56), residues: 71
  sheet: -0.70 (0.54), residues: 100
  loop : -1.50 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.015   0.002   TYR B 156 
 PHE   0.008   0.001   PHE B 101 
 TRP   0.009   0.001   TRP B 375 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3620)
  covalent geometry    : angle       0.70657 ( 4869)
  SS BOND              : bond        0.00514 (   11)
  SS BOND              : angle       1.69992 (   22)
  hydrogen bonds       : bond        0.03289 (  114)
  hydrogen bonds       : angle       5.76719 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.5774 (OUTLIER) cc_final: 0.4934 (mt)
REVERT: B  206 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6162 (tp)
REVERT: B  219 GLU cc_start: 0.7360 (mp0) cc_final: 0.7135 (mp0)
REVERT: B  228 MET cc_start: 0.8671 (mtt) cc_final: 0.8330 (mtp)
REVERT: B  234 HIS cc_start: 0.7169 (t70) cc_final: 0.6763 (t-90)
REVERT: B  247 MET cc_start: 0.6083 (ttm) cc_final: 0.5852 (tpt)
REVERT: B  379 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7988 (p)
REVERT: A   43 MET cc_start: 0.5326 (mpm) cc_final: 0.5052 (tpp)
  outliers start: 19
  outliers final: 11
  residues processed: 60
  average time/residue: 0.4446
  time to fit residues: 27.7561
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.187835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.165683 restraints weight = 6508.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4675 rms_B_bonded: 4.06
r_work: 0.4527 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5910
moved from start:          0.5910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3631  Z= 0.150
  Angle     :  0.744   9.126   4891  Z= 0.384
  Chirality :  0.047   0.234    529
  Planarity :  0.005   0.054    623
  Dihedral  :  5.334  24.862    469
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 28.72 %
    Favored  : 66.92 %
  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 are not related in a simple way.
  whole: -1.92 (0.41), residues: 427
  helix: -1.29 (0.59), residues: 71
  sheet: -0.94 (0.50), residues: 113
  loop : -1.41 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 105 
 TYR   0.016   0.002   TYR B 156 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B 375 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3620)
  covalent geometry    : angle       0.73509 ( 4869)
  SS BOND              : bond        0.00473 (   11)
  SS BOND              : angle       1.89464 (   22)
  hydrogen bonds       : bond        0.03432 (  114)
  hydrogen bonds       : angle       5.75572 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.5713 (OUTLIER) cc_final: 0.4929 (mt)
REVERT: B  206 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6255 (tp)
REVERT: B  212 GLU cc_start: 0.8373 (tt0) cc_final: 0.7900 (mp0)
REVERT: B  219 GLU cc_start: 0.7389 (mp0) cc_final: 0.7160 (mp0)
REVERT: B  228 MET cc_start: 0.8714 (mtt) cc_final: 0.8409 (mtp)
REVERT: B  234 HIS cc_start: 0.7170 (t70) cc_final: 0.6745 (t-90)
REVERT: B  247 MET cc_start: 0.6108 (ttm) cc_final: 0.5864 (tpt)
REVERT: B  379 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8008 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 60
  average time/residue: 0.4218
  time to fit residues: 26.3308
Evaluate side-chains
  58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 CYS
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0670
   chunk 1 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 GLN ** 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 = 0.4970 r_free = 0.4970 target = 0.189643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.167441 restraints weight = 6775.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.4701 rms_B_bonded: 4.15
r_work: 0.4552 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.4552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5877
moved from start:          0.6110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3631  Z= 0.143
  Angle     :  0.781  10.194   4891  Z= 0.398
  Chirality :  0.048   0.226    529
  Planarity :  0.005   0.054    623
  Dihedral  :  5.363  23.835    469
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 28.97 %
    Favored  : 67.69 %
  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 are not related in a simple way.
  whole: -1.88 (0.41), residues: 427
  helix: -1.34 (0.58), residues: 71
  sheet: -0.98 (0.50), residues: 107
  loop : -1.32 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.016   0.001   TYR B 156 
 PHE   0.007   0.001   PHE B 101 
 TRP   0.007   0.001   TRP B 375 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3620)
  covalent geometry    : angle       0.77227 ( 4869)
  SS BOND              : bond        0.00511 (   11)
  SS BOND              : angle       1.94010 (   22)
  hydrogen bonds       : bond        0.03432 (  114)
  hydrogen bonds       : angle       5.78576 (  285)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 ILE cc_start: 0.5664 (OUTLIER) cc_final: 0.4925 (mt)
REVERT: B  219 GLU cc_start: 0.7395 (mp0) cc_final: 0.7168 (mp0)
REVERT: B  228 MET cc_start: 0.8688 (mtt) cc_final: 0.8330 (mtp)
REVERT: B  234 HIS cc_start: 0.7441 (t70) cc_final: 0.7185 (t-90)
REVERT: B  236 ASP cc_start: 0.6748 (m-30) cc_final: 0.6226 (t70)
REVERT: B  247 MET cc_start: 0.6094 (ttm) cc_final: 0.5863 (tpt)
REVERT: B  379 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8006 (p)
REVERT: A   43 MET cc_start: 0.5802 (tpp) cc_final: 0.4911 (tpp)
  outliers start: 13
  outliers final: 9
  residues processed: 58
  average time/residue: 0.4041
  time to fit residues: 24.4612
Evaluate side-chains
  57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  116 MET
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  30 ASN
** B  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.180427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.156341 restraints weight = 6520.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.4542 rms_B_bonded: 4.17
r_work: 0.4389 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6018
moved from start:          0.5895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   3631  Z= 0.290
  Angle     :  0.949  12.744   4891  Z= 0.487
  Chirality :  0.055   0.254    529
  Planarity :  0.006   0.053    623
  Dihedral  :  6.352  29.755    469
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 21.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 29.23 %
    Favored  : 66.92 %
  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 are not related in a simple way.
  whole: -2.22 (0.38), residues: 427
  helix: -1.42 (0.61), residues: 71
  sheet: -0.59 (0.51), residues: 99
  loop : -1.92 (0.36), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 314 
 TYR   0.027   0.003   TYR B 156 
 PHE   0.017   0.003   PHE B 260 
 TRP   0.011   0.002   TRP B  49 
 HIS   0.007   0.002   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 3620)
  covalent geometry    : angle       0.92062 ( 4869)
  SS BOND              : bond        0.01083 (   11)
  SS BOND              : angle       3.57212 (   22)
  hydrogen bonds       : bond        0.04508 (  114)
  hydrogen bonds       : angle       6.31723 (  285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1976.38 seconds
wall clock time: 34 minutes 18.91 seconds (2058.91 seconds total)