Starting phenix.real_space_refine
on Fri Aug 22 15:02:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ym8_33924/08_2025/7ym8_33924.cif"
  }
  resolution = 2.92
  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=   0.001 sd=   0.109
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      26      5.16       5
     C    2805      2.51       5
     N     704      2.21       5
     O     752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 4287
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1238
          Classifications: {'peptide': 169}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 1, 'TRANS': 167}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 212
          Unresolved non-hydrogen dihedrals: 143
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "A"
      Number of atoms: 2108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2108
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 14, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 887
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'J5C': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.37, per 1000 atoms: 0.32
  Number of scatterers: 4287
  At special positions: 0
  Unit cell: (59.5375, 58.455, 138.56, 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      26     16.00
     O     752      8.00
     N     704      7.00
     C    2805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  94 " distance=2.03

  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: 0.34
  Conformation dependent library (CDL) restraints added in 152.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1038

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      51.8% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 27 through 33
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 3.666A  pdb=" N   CYS B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 113
    Processing helix  chain 'B' and resid 128 through 133
      removed outlier: 3.708A  pdb=" N   ALA B 132 " --> pdb=" O   GLN B 128 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU B 133 " --> pdb=" O   ASP B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 133'
    Processing helix  chain 'B' and resid 169 through 184
      removed outlier: 4.243A  pdb=" N   PHE B 174 " --> pdb=" O   ARG B 170 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   ILE B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG B 176 " --> pdb=" O   LYS B 172 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE B 179 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.722A  pdb=" N   ARG B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 53
      removed outlier: 3.586A  pdb=" N   ILE A  48 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   CYS A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 79
      removed outlier: 3.664A  pdb=" N   ILE A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A  68 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 95 through 129
    Processing helix  chain 'A' and resid 141 through 159
    Processing helix  chain 'A' and resid 184 through 211
      removed outlier: 5.603A  pdb=" N   LEU A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      Proline residue:  A 196  - end of helix
    Processing helix  chain 'A' and resid 263 through 286
      removed outlier: 3.931A  pdb=" N   GLU A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LYS A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE A 281 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      Proline residue:  A 293  - end of helix
    Processing helix  chain 'A' and resid 304 through 326
      removed outlier: 3.775A  pdb=" N   PHE A 308 " --> pdb=" O   SER A 304 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLY A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   SER A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   CYS A 320 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 327 through 329
      No H-bonds generated for 'chain 'A' and resid 327 through 329'
    Processing helix  chain 'A' and resid 330 through 341
      removed outlier: 3.875A  pdb=" N   GLN A 338 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ASN A 339 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58
      removed outlier: 9.826A  pdb=" N   ALA B  87 " --> pdb=" O   THR B  15 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ARG B  17 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ILE B  89 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU B  19 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   VAL B  91 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 6 through 7
    Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 13
      removed outlier: 3.585A  pdb=" N   SER D 115 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   MET D  34 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    705 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: 0.59

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 669
        1.32 -     1.44: 1248
        1.44 -     1.56: 2438
        1.56 -     1.68: 1
        1.68 -     1.81: 35
  Bond restraints: 4391
  Sorted by residual:
  bond pdb=" C9  J5C A 501 "
       pdb=" N13 J5C A 501 "
    ideal  model  delta    sigma   weight residual
    1.277  1.463 -0.186 2.00e-02 2.50e+03 8.67e+01
  bond pdb=" C9  J5C A 501 "
       pdb=" N10 J5C A 501 "
    ideal  model  delta    sigma   weight residual
    1.373  1.465 -0.092 2.00e-02 2.50e+03 2.11e+01
  bond pdb=" C11 J5C A 501 "
       pdb=" C12 J5C A 501 "
    ideal  model  delta    sigma   weight residual
    1.540  1.490  0.050 2.00e-02 2.50e+03 6.37e+00
  bond pdb=" C5  J5C A 501 "
       pdb=" O15 J5C A 501 "
    ideal  model  delta    sigma   weight residual
    1.356  1.400 -0.044 2.00e-02 2.50e+03 4.89e+00
  bond pdb=" C   MET A 292 "
       pdb=" N   PRO A 293 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.043 2.34e-02 1.83e+03 3.31e+00
  ... (remaining 4386 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 5724
        1.78 -     3.56: 211
        3.56 -     5.34: 37
        5.34 -     7.13: 13
        7.13 -     8.91: 4
  Bond angle restraints: 5989
  Sorted by residual:
  angle pdb=" C   ARG B 117 "
        pdb=" N   THR B 118 "
        pdb=" CA  THR B 118 "
      ideal   model   delta    sigma   weight residual
     122.46  127.56   -5.10 1.41e+00 5.03e-01 1.31e+01
  angle pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
        pdb=" C   LEU A  80 "
      ideal   model   delta    sigma   weight residual
     109.81  117.34   -7.53 2.21e+00 2.05e-01 1.16e+01
  angle pdb=" CA  THR B 118 "
        pdb=" CB  THR B 118 "
        pdb=" CG2 THR B 118 "
      ideal   model   delta    sigma   weight residual
     110.50  115.96   -5.46 1.70e+00 3.46e-01 1.03e+01
  angle pdb=" N   ASN A 322 "
        pdb=" CA  ASN A 322 "
        pdb=" C   ASN A 322 "
      ideal   model   delta    sigma   weight residual
     113.16  117.48   -4.32 1.42e+00 4.96e-01 9.26e+00
  angle pdb=" N10 J5C A 501 "
        pdb=" C9  J5C A 501 "
        pdb=" N13 J5C A 501 "
      ideal   model   delta    sigma   weight residual
     116.22  107.31    8.91 3.00e+00 1.11e-01 8.82e+00
  ... (remaining 5984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.45: 2347
       20.45 -    40.90: 199
       40.90 -    61.34: 34
       61.34 -    81.79: 8
       81.79 -   102.24: 3
  Dihedral angle restraints: 2591
    sinusoidal: 976
      harmonic: 1615
  Sorted by residual:
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  94 "
           pdb=" CB  CYS D  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.87   33.13     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CA  ILE A 325 "
           pdb=" C   ILE A 325 "
           pdb=" N   TYR A 326 "
           pdb=" CA  TYR A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.10  -18.90     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CAR Y01 A 502 "
           pdb=" CAV Y01 A 502 "
           pdb=" CBC Y01 A 502 "
           pdb=" CAZ Y01 A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.40  -46.84  102.24     1      3.00e+01 1.11e-03 1.29e+01
  ... (remaining 2588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 411
       0.038 -    0.077: 191
       0.077 -    0.115: 67
       0.115 -    0.154: 16
       0.154 -    0.192: 7
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B  85 "
            pdb=" CA  VAL B  85 "
            pdb=" CG1 VAL B  85 "
            pdb=" CG2 VAL B  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.21e-01
  chirality pdb=" CA  THR B 118 "
            pdb=" N   THR B 118 "
            pdb=" C   THR B 118 "
            pdb=" CB  THR B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" CB  ILE A 126 "
            pdb=" CA  ILE A 126 "
            pdb=" CG1 ILE A 126 "
            pdb=" CG2 ILE A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.68e-01
  ... (remaining 689 not shown)

  Planarity restraints: 740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  80 "   -0.041 5.00e-02 4.00e+02   6.11e-02 5.98e+00
        pdb=" N   PRO A  81 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  81 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  81 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 326 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO A 327 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 286 "   -0.038 5.00e-02 4.00e+02   5.61e-02 5.04e+00
        pdb=" N   PRO A 287 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 737 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1415
        2.84 -     3.36: 3748
        3.36 -     3.87: 7189
        3.87 -     4.39: 8184
        4.39 -     4.90: 14266
  Nonbonded interactions: 34802
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  74 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   ALA B  23 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   SER D  83 "
            pdb=" OG  SER D  83 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" NH2 ARG A 124 "
            pdb=" OG  SER A 329 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   GLN B 101 "
            pdb=" ND2 ASN B 105 "
     model   vdw
     2.396 3.120
  ... (remaining 34797 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:             1.270
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.230
  Find NCS groups from input model:        0.020
  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:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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      :  0.006   0.186   4393  Z= 0.292
  Angle     :  0.860   8.907   5993  Z= 0.462
  Chirality :  0.051   0.192    692
  Planarity :  0.007   0.061    740
  Dihedral  : 16.010 102.240   1547
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  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: -3.62 (0.30), residues: 544
  helix: -2.14 (0.24), residues: 271
  sheet: -1.98 (0.50), residues: 100
  loop : -2.68 (0.41), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 101 
 TYR   0.035   0.002   TYR D  37 
 PHE   0.017   0.002   PHE A  94 
 TRP   0.013   0.002   TRP A 165 
 HIS   0.005   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 4391)
  covalent geometry    : angle       0.86015 ( 5989)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.59332 (    4)
  hydrogen bonds       : bond        0.14542 (  240)
  hydrogen bonds       : angle       7.40661 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.109 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7150 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7899 (mt) cc_final: 0.7671 (mp)
REVERT: B  204 GLU cc_start: 0.6596 (mp0) cc_final: 0.6389 (mp0)
REVERT: A   61 THR cc_start: 0.8518 (m) cc_final: 0.8288 (p)
REVERT: A  203 MET cc_start: 0.8882 (mmp) cc_final: 0.8631 (mmm)
REVERT: D  105 TYR cc_start: 0.7753 (m-10) cc_final: 0.7372 (m-10)
  outliers start: 0
  outliers final: 1
  residues processed: 74
  average time/residue: 0.3704
  time to fit residues: 28.6802
Evaluate side-chains
  56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  110 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 112 ASN
B 226 ASN
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 HIS
D 111 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.171363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.130027 restraints weight = 4421.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.63
r_work: 0.3114 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4393  Z= 0.157
  Angle     :  0.571   5.697   5993  Z= 0.296
  Chirality :  0.043   0.135    692
  Planarity :  0.005   0.046    740
  Dihedral  :  9.848  83.463    681
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.72 %
    Favored  : 83.72 %
  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: -1.84 (0.34), residues: 544
  helix: -0.37 (0.29), residues: 276
  sheet: -1.59 (0.52), residues: 101
  loop : -2.18 (0.45), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.017   0.001   TYR D  37 
 PHE   0.013   0.002   PHE A  94 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4391)
  covalent geometry    : angle       0.57066 ( 5989)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       0.43046 (    4)
  hydrogen bonds       : bond        0.04708 (  240)
  hydrogen bonds       : angle       5.25642 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.162 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7492 (ttm110)
REVERT: B  226 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7482 (t0)
REVERT: A   61 THR cc_start: 0.8753 (m) cc_final: 0.8409 (p)
REVERT: A  203 MET cc_start: 0.9092 (mmp) cc_final: 0.8809 (mmm)
  outliers start: 11
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3899
  time to fit residues: 27.4966
Evaluate side-chains
  64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 ASN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0770
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.174097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131529 restraints weight = 4392.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.61
r_work: 0.3140 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4393  Z= 0.107
  Angle     :  0.519   8.153   5993  Z= 0.265
  Chirality :  0.041   0.125    692
  Planarity :  0.004   0.042    740
  Dihedral  :  8.686  63.785    679
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.74 %
    Favored  : 80.93 %
  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: -0.82 (0.36), residues: 544
  helix:  0.53 (0.31), residues: 277
  sheet: -1.16 (0.53), residues: 101
  loop : -1.83 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.010   0.001   TYR D  53 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 4391)
  covalent geometry    : angle       0.51922 ( 5989)
  SS BOND              : bond        0.00028 (    2)
  SS BOND              : angle       0.42744 (    4)
  hydrogen bonds       : bond        0.03929 (  240)
  hydrogen bonds       : angle       4.83488 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.173 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7242 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7866 (mt) cc_final: 0.7559 (mp)
REVERT: B  226 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7443 (t0)
REVERT: A   31 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (t)
REVERT: A   36 LEU cc_start: 0.8003 (mt) cc_final: 0.7538 (tp)
REVERT: A   61 THR cc_start: 0.8712 (m) cc_final: 0.8385 (p)
REVERT: A  162 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7262 (tp)
REVERT: A  203 MET cc_start: 0.9062 (mmp) cc_final: 0.8728 (mmm)
REVERT: A  294 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (mp)
REVERT: A  305 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7200 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 62
  average time/residue: 0.4198
  time to fit residues: 27.2623
Evaluate side-chains
  61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  226 ASN
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    0.2980
   chunk 6 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.170963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.128547 restraints weight = 4366.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.62
r_work: 0.3097 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4393  Z= 0.153
  Angle     :  0.538   5.838   5993  Z= 0.276
  Chirality :  0.042   0.123    692
  Planarity :  0.004   0.041    740
  Dihedral  :  7.366  63.788    679
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.98 %
    Favored  : 79.77 %
  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: -0.61 (0.36), residues: 544
  helix:  0.68 (0.31), residues: 277
  sheet: -1.06 (0.53), residues: 101
  loop : -1.68 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 166 
 TYR   0.016   0.001   TYR D  37 
 PHE   0.012   0.001   PHE A  94 
 TRP   0.007   0.001   TRP A 165 
 HIS   0.003   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4391)
  covalent geometry    : angle       0.53800 ( 5989)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.48929 (    4)
  hydrogen bonds       : bond        0.04218 (  240)
  hydrogen bonds       : angle       4.81430 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.137 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7222 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7892 (mt) cc_final: 0.7523 (mp)
REVERT: B  176 ARG cc_start: 0.6530 (ttp-170) cc_final: 0.6313 (ttp-170)
REVERT: B  182 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6829 (mp)
REVERT: B  202 ASP cc_start: 0.6216 (t0) cc_final: 0.5877 (t70)
REVERT: B  204 GLU cc_start: 0.6482 (mp0) cc_final: 0.6135 (mp0)
REVERT: B  226 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7425 (t0)
REVERT: A   36 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7521 (tp)
REVERT: A   61 THR cc_start: 0.8768 (m) cc_final: 0.8331 (p)
REVERT: A  162 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7285 (tp)
REVERT: A  203 MET cc_start: 0.9077 (mmp) cc_final: 0.8779 (mmm)
REVERT: A  294 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7387 (mp)
REVERT: A  305 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7174 (tt0)
  outliers start: 14
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4361
  time to fit residues: 32.3676
Evaluate side-chains
  70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  226 ASN
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0670
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
B 226 ASN
** A 179 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.168699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.124564 restraints weight = 4417.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.67
r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4393  Z= 0.136
  Angle     :  0.515   5.675   5993  Z= 0.265
  Chirality :  0.042   0.124    692
  Planarity :  0.004   0.041    740
  Dihedral  :  7.072  63.660    679
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.37 %
    Favored  : 79.07 %
  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 (0.37), residues: 544
  helix:  0.86 (0.31), residues: 276
  sheet: -0.98 (0.53), residues: 101
  loop : -1.54 (0.48), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.018   0.001   TYR D  53 
 PHE   0.011   0.001   PHE A  94 
 TRP   0.007   0.001   TRP A 165 
 HIS   0.002   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4391)
  covalent geometry    : angle       0.51526 ( 5989)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       0.49176 (    4)
  hydrogen bonds       : bond        0.04092 (  240)
  hydrogen bonds       : angle       4.72888 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.157 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7185 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7872 (mt) cc_final: 0.7494 (mp)
REVERT: B  182 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6686 (mp)
REVERT: A   36 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7485 (tp)
REVERT: A  162 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7315 (tp)
REVERT: A  203 MET cc_start: 0.9054 (mmp) cc_final: 0.8742 (mmm)
REVERT: A  205 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7365 (m)
REVERT: A  294 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7341 (mp)
REVERT: A  305 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7216 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 66
  average time/residue: 0.3974
  time to fit residues: 27.4898
Evaluate side-chains
  69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 30 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 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 = 0.3813 r_free = 0.3813 target = 0.168158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.125479 restraints weight = 4525.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.91
r_work: 0.3068 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4393  Z= 0.131
  Angle     :  0.504   5.582   5993  Z= 0.260
  Chirality :  0.042   0.125    692
  Planarity :  0.004   0.040    740
  Dihedral  :  7.001  63.769    679
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.67 %
    Favored  : 78.84 %
  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 (0.37), residues: 544
  helix:  1.00 (0.32), residues: 276
  sheet: -0.86 (0.53), residues: 101
  loop : -1.41 (0.49), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.021   0.001   TYR D  53 
 PHE   0.011   0.001   PHE A  94 
 TRP   0.006   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4391)
  covalent geometry    : angle       0.50369 ( 5989)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.48048 (    4)
  hydrogen bonds       : bond        0.03992 (  240)
  hydrogen bonds       : angle       4.64428 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.165 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7246 (ttp-110)
REVERT: B  182 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6745 (mp)
REVERT: B  226 ASN cc_start: 0.8443 (m110) cc_final: 0.7528 (t0)
REVERT: A   36 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7486 (tp)
REVERT: A  162 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7289 (tp)
REVERT: A  203 MET cc_start: 0.9074 (mmp) cc_final: 0.8769 (mmm)
REVERT: A  205 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7413 (m)
REVERT: A  294 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7373 (mp)
REVERT: A  305 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7207 (tt0)
  outliers start: 15
  outliers final: 7
  residues processed: 67
  average time/residue: 0.4262
  time to fit residues: 29.9290
Evaluate side-chains
  68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0270
   chunk 44 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0670
   chunk 15 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0050
   chunk 51 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.173952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.132136 restraints weight = 4471.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.64
r_work: 0.3140 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4393  Z= 0.104
  Angle     :  0.477   5.124   5993  Z= 0.247
  Chirality :  0.041   0.124    692
  Planarity :  0.004   0.038    740
  Dihedral  :  6.883  64.318    679
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.77 %
    Favored  : 77.67 %
  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:  0.14 (0.38), residues: 544
  helix:  1.22 (0.32), residues: 278
  sheet: -0.68 (0.54), residues: 101
  loop : -1.26 (0.50), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 181 
 TYR   0.021   0.001   TYR D  53 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.005   0.001   TRP A 102 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4391)
  covalent geometry    : angle       0.47713 ( 5989)
  SS BOND              : bond        0.00069 (    2)
  SS BOND              : angle       0.43774 (    4)
  hydrogen bonds       : bond        0.03650 (  240)
  hydrogen bonds       : angle       4.48511 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.153 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7275 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7794 (mt) cc_final: 0.7545 (mp)
REVERT: B  182 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6743 (mp)
REVERT: B  226 ASN cc_start: 0.8334 (m110) cc_final: 0.7464 (t0)
REVERT: A   36 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7558 (tp)
REVERT: A  162 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7276 (tp)
REVERT: A  203 MET cc_start: 0.9052 (mmp) cc_final: 0.8722 (mmm)
REVERT: A  205 CYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7357 (m)
REVERT: A  294 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7373 (mp)
REVERT: A  305 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7263 (tt0)
  outliers start: 11
  outliers final: 4
  residues processed: 70
  average time/residue: 0.3796
  time to fit residues: 27.8030
Evaluate side-chains
  69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.167847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.124592 restraints weight = 4467.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.75
r_work: 0.3102 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4393  Z= 0.139
  Angle     :  0.519   5.690   5993  Z= 0.267
  Chirality :  0.042   0.134    692
  Planarity :  0.004   0.038    740
  Dihedral  :  6.971  63.594    679
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.53 %
    Favored  : 77.44 %
  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:  0.06 (0.37), residues: 544
  helix:  1.13 (0.32), residues: 278
  sheet: -0.66 (0.54), residues: 101
  loop : -1.27 (0.50), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 166 
 TYR   0.024   0.001   TYR D  53 
 PHE   0.011   0.001   PHE A  94 
 TRP   0.006   0.001   TRP A 165 
 HIS   0.002   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4391)
  covalent geometry    : angle       0.51941 ( 5989)
  SS BOND              : bond        0.00081 (    2)
  SS BOND              : angle       0.49655 (    4)
  hydrogen bonds       : bond        0.03982 (  240)
  hydrogen bonds       : angle       4.57433 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.158 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7325 (ttp-110)
REVERT: B  182 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6790 (mp)
REVERT: B  226 ASN cc_start: 0.8391 (m110) cc_final: 0.7570 (t0)
REVERT: A   36 LEU cc_start: 0.8021 (mt) cc_final: 0.7578 (tp)
REVERT: A  162 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7225 (tp)
REVERT: A  203 MET cc_start: 0.9064 (mmp) cc_final: 0.8782 (mmm)
REVERT: A  205 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7420 (m)
REVERT: A  294 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7448 (mp)
REVERT: A  305 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7281 (tt0)
  outliers start: 13
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3921
  time to fit residues: 27.4681
Evaluate side-chains
  68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0070
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.170444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.126046 restraints weight = 4441.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.73
r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4393  Z= 0.110
  Angle     :  0.491   5.103   5993  Z= 0.253
  Chirality :  0.041   0.130    692
  Planarity :  0.003   0.038    740
  Dihedral  :  6.896  63.975    679
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.00 %
    Favored  : 77.44 %
  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:  0.20 (0.38), residues: 544
  helix:  1.25 (0.32), residues: 278
  sheet: -0.50 (0.55), residues: 97
  loop : -1.27 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.023   0.001   TYR D  53 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.006   0.001   TRP D 106 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4391)
  covalent geometry    : angle       0.49142 ( 5989)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.43902 (    4)
  hydrogen bonds       : bond        0.03730 (  240)
  hydrogen bonds       : angle       4.47162 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.163 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7300 (ttp-110)
REVERT: B   21 LEU cc_start: 0.7814 (mt) cc_final: 0.7516 (mp)
REVERT: B  182 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6687 (mp)
REVERT: B  226 ASN cc_start: 0.8401 (m110) cc_final: 0.7562 (t0)
REVERT: A   36 LEU cc_start: 0.8019 (mt) cc_final: 0.7570 (tp)
REVERT: A  162 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7146 (tp)
REVERT: A  203 MET cc_start: 0.9061 (mmp) cc_final: 0.8748 (mmm)
REVERT: A  205 CYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7398 (m)
REVERT: A  294 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7421 (mp)
REVERT: A  305 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7244 (tt0)
  outliers start: 11
  outliers final: 4
  residues processed: 66
  average time/residue: 0.4132
  time to fit residues: 28.5284
Evaluate side-chains
  66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.170672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.128645 restraints weight = 4448.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.68
r_work: 0.3091 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4393  Z= 0.167
  Angle     :  0.544   6.032   5993  Z= 0.279
  Chirality :  0.043   0.123    692
  Planarity :  0.004   0.038    740
  Dihedral  :  7.070  63.116    679
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.77 %
    Favored  : 77.67 %
  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: -0.04 (0.37), residues: 544
  helix:  1.06 (0.32), residues: 275
  sheet: -0.58 (0.55), residues: 97
  loop : -1.38 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 166 
 TYR   0.026   0.002   TYR D  53 
 PHE   0.012   0.002   PHE A  94 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4391)
  covalent geometry    : angle       0.54437 ( 5989)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.55057 (    4)
  hydrogen bonds       : bond        0.04188 (  240)
  hydrogen bonds       : angle       4.62499 (  705)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.156 
Fit side-chains
REVERT: B   17 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7418 (ttp-110)
REVERT: B  182 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6874 (mp)
REVERT: B  226 ASN cc_start: 0.8424 (m110) cc_final: 0.7615 (t0)
REVERT: A   36 LEU cc_start: 0.8023 (mt) cc_final: 0.7591 (tp)
REVERT: A  203 MET cc_start: 0.9083 (mmp) cc_final: 0.8828 (mmm)
REVERT: A  205 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7426 (m)
REVERT: A  294 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7513 (mp)
REVERT: A  305 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7307 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 0.4219
  time to fit residues: 30.0977
Evaluate side-chains
  69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  305 GLU
Chi-restraints excluded: chain D residue   21 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.171274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.129110 restraints weight = 4484.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.61
r_work: 0.3135 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4393  Z= 0.145
  Angle     :  0.535   6.688   5993  Z= 0.272
  Chirality :  0.042   0.124    692
  Planarity :  0.004   0.038    740
  Dihedral  :  7.049  63.538    679
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.93 %
    Favored  : 76.98 %
  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:  0.06 (0.37), residues: 544
  helix:  1.17 (0.32), residues: 274
  sheet: -0.48 (0.55), residues: 97
  loop : -1.40 (0.47), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 166 
 TYR   0.025   0.001   TYR D  53 
 PHE   0.011   0.001   PHE B  56 
 TRP   0.007   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4391)
  covalent geometry    : angle       0.53494 ( 5989)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.49311 (    4)
  hydrogen bonds       : bond        0.04039 (  240)
  hydrogen bonds       : angle       4.59732 (  705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1587.64 seconds
wall clock time: 27 minutes 42.92 seconds (1662.92 seconds total)