Starting phenix.real_space_refine on Tue Jun 25 20:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x16_37985/06_2024/8x16_37985_updated.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.071 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5615 2.51 5 N 1468 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8751 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2268 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'Q8L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.63 Number of scatterers: 8751 At special positions: 0 Unit cell: (118.656, 92.288, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 68 16.00 O 1599 8.00 N 1468 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 33.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'R' and resid 10 through 39 Processing helix chain 'R' and resid 41 through 43 No H-bonds generated for 'chain 'R' and resid 41 through 43' Processing helix chain 'R' and resid 48 through 63 removed outlier: 3.787A pdb=" N SER R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 74 Processing helix chain 'R' and resid 80 through 113 removed outlier: 4.947A pdb=" N PHE R 85 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 121 removed outlier: 3.598A pdb=" N TYR R 118 " --> pdb=" O THR R 115 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS R 119 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 142 Processing helix chain 'R' and resid 145 through 147 No H-bonds generated for 'chain 'R' and resid 145 through 147' Processing helix chain 'R' and resid 182 through 185 No H-bonds generated for 'chain 'R' and resid 182 through 185' Processing helix chain 'R' and resid 187 through 208 Processing helix chain 'R' and resid 223 through 254 Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 261 through 281 removed outlier: 3.840A pdb=" N ASN R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET R 276 " --> pdb=" O HIS R 272 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 284 through 286 No H-bonds generated for 'chain 'R' and resid 284 through 286' Processing helix chain 'R' and resid 289 through 298 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.751A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.129A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 122 through 125 Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.674A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.582A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.909A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.343A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'H' and resid 226 through 231 removed outlier: 3.592A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1086 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: 2.29 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 2836 1.37 - 1.55: 5994 1.55 - 1.74: 4 1.74 - 1.92: 101 1.92 - 2.11: 1 Bond restraints: 8936 Sorted by residual: bond pdb=" C5 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.419 1.667 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1 Q8L R 401 " pdb=" C5 Q8L R 401 " ideal model delta sigma weight residual 1.530 1.286 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.432 1.299 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" N Q8L R 401 " pdb=" C3 Q8L R 401 " ideal model delta sigma weight residual 1.338 1.452 -0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C10 Q8L R 401 " pdb=" N5 Q8L R 401 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.70: 272 107.70 - 114.84: 5337 114.84 - 121.98: 4657 121.98 - 129.12: 1783 129.12 - 136.26: 68 Bond angle restraints: 12117 Sorted by residual: angle pdb=" C GLN R 167 " pdb=" N PHE R 168 " pdb=" CA PHE R 168 " ideal model delta sigma weight residual 121.54 136.26 -14.72 1.91e+00 2.74e-01 5.94e+01 angle pdb=" CA GLN R 167 " pdb=" C GLN R 167 " pdb=" O GLN R 167 " ideal model delta sigma weight residual 120.52 111.74 8.78 1.39e+00 5.18e-01 3.99e+01 angle pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" C SER R 82 " ideal model delta sigma weight residual 111.02 101.47 9.55 1.52e+00 4.33e-01 3.95e+01 angle pdb=" N TYR R 81 " pdb=" CA TYR R 81 " pdb=" C TYR R 81 " ideal model delta sigma weight residual 112.97 106.71 6.26 1.06e+00 8.90e-01 3.49e+01 angle pdb=" N CYS R 166 " pdb=" CA CYS R 166 " pdb=" C CYS R 166 " ideal model delta sigma weight residual 108.73 116.17 -7.44 1.63e+00 3.76e-01 2.08e+01 ... (remaining 12112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5113 17.60 - 35.21: 140 35.21 - 52.81: 27 52.81 - 70.42: 2 70.42 - 88.02: 1 Dihedral angle restraints: 5283 sinusoidal: 2009 harmonic: 3274 Sorted by residual: dihedral pdb=" C SER R 82 " pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" CB SER R 82 " ideal model delta harmonic sigma weight residual -122.60 -115.20 -7.40 0 2.50e+00 1.60e-01 8.76e+00 dihedral pdb=" CA SER R 242 " pdb=" C SER R 242 " pdb=" N TRP R 243 " pdb=" CA TRP R 243 " ideal model delta harmonic sigma weight residual -180.00 -166.08 -13.92 0 5.00e+00 4.00e-02 7.75e+00 dihedral pdb=" N GLN R 167 " pdb=" CA GLN R 167 " pdb=" CB GLN R 167 " pdb=" CG GLN R 167 " ideal model delta sinusoidal sigma weight residual -180.00 -136.96 -43.04 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1268 0.062 - 0.124: 125 0.124 - 0.186: 5 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CG LEU R 164 " pdb=" CB LEU R 164 " pdb=" CD1 LEU R 164 " pdb=" CD2 LEU R 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU R 164 " pdb=" N LEU R 164 " pdb=" C LEU R 164 " pdb=" CB LEU R 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA CYS R 166 " pdb=" N CYS R 166 " pdb=" C CYS R 166 " pdb=" CB CYS R 166 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1399 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 80 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C PHE R 80 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE R 80 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR R 81 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO H 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 164 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C LEU R 164 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU R 164 " 0.009 2.00e-02 2.50e+03 pdb=" N SER R 165 " 0.008 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 975 2.75 - 3.31: 8983 3.31 - 3.86: 15059 3.86 - 4.41: 18046 4.41 - 4.96: 30945 Nonbonded interactions: 74008 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.203 2.440 nonbonded pdb=" CD1 PHE R 182 " pdb=" OG SER R 247 " model vdw 2.260 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.287 2.440 nonbonded pdb=" O VAL R 141 " pdb=" OH TYR R 176 " model vdw 2.292 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.313 2.520 ... (remaining 74003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.800 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: 3.570 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 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 : 0.005 0.248 8936 Z= 0.328 Angle : 0.531 14.721 12117 Z= 0.302 Chirality : 0.041 0.310 1402 Planarity : 0.003 0.037 1507 Dihedral : 8.098 88.024 3168 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Rotamer: Outliers : 0.32 % Allowed : 4.80 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1108 helix: 0.28 (0.25), residues: 396 sheet: -0.61 (0.30), residues: 263 loop : -1.82 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.000 HIS H 35 PHE 0.009 0.001 PHE A 189 TYR 0.006 0.001 TYR H 102 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 311 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.6825 (m) cc_final: 0.6518 (m) REVERT: R 175 ASP cc_start: 0.7181 (p0) cc_final: 0.6514 (p0) REVERT: A 302 TYR cc_start: 0.7277 (t80) cc_final: 0.6885 (t80) outliers start: 3 outliers final: 1 residues processed: 314 average time/residue: 0.2334 time to fit residues: 95.9622 Evaluate side-chains 188 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS A 306 GLN B 16 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 293 ASN C 24 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8936 Z= 0.249 Angle : 0.615 7.764 12117 Z= 0.314 Chirality : 0.044 0.198 1402 Planarity : 0.004 0.065 1507 Dihedral : 4.845 87.676 1242 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.09 % Allowed : 15.03 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1108 helix: 1.13 (0.27), residues: 394 sheet: -0.42 (0.30), residues: 276 loop : -1.47 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 243 HIS 0.005 0.001 HIS R 158 PHE 0.020 0.002 PHE A 191 TYR 0.019 0.002 TYR H 60 ARG 0.008 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 168 PHE cc_start: 0.7383 (t80) cc_final: 0.7156 (t80) REVERT: R 173 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.7114 (mtp-110) REVERT: R 190 LEU cc_start: 0.8214 (tt) cc_final: 0.7713 (tt) REVERT: R 197 TYR cc_start: 0.7033 (m-80) cc_final: 0.6375 (m-80) outliers start: 29 outliers final: 15 residues processed: 231 average time/residue: 0.2085 time to fit residues: 66.4102 Evaluate side-chains 185 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS A 52 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8936 Z= 0.378 Angle : 0.683 8.031 12117 Z= 0.353 Chirality : 0.046 0.194 1402 Planarity : 0.004 0.073 1507 Dihedral : 5.570 87.349 1240 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.58 % Allowed : 16.20 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1108 helix: 1.03 (0.26), residues: 397 sheet: -0.41 (0.30), residues: 266 loop : -1.16 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.048 0.003 HIS R 124 PHE 0.018 0.002 PHE R 182 TYR 0.018 0.002 TYR B 145 ARG 0.014 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8253 (mt0) cc_final: 0.7940 (mp10) REVERT: R 173 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7296 (mtp85) REVERT: R 197 TYR cc_start: 0.7775 (m-80) cc_final: 0.7070 (m-80) REVERT: A 247 MET cc_start: 0.6351 (ptt) cc_final: 0.6045 (ptm) REVERT: B 142 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6302 (m90) REVERT: B 160 SER cc_start: 0.8221 (m) cc_final: 0.7889 (t) REVERT: B 169 TRP cc_start: 0.7928 (m100) cc_final: 0.7599 (m100) outliers start: 43 outliers final: 27 residues processed: 222 average time/residue: 0.2100 time to fit residues: 63.3337 Evaluate side-chains 188 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS A 52 GLN A 304 GLN A 322 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8936 Z= 0.264 Angle : 0.597 7.654 12117 Z= 0.306 Chirality : 0.044 0.211 1402 Planarity : 0.004 0.064 1507 Dihedral : 5.034 80.929 1240 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.37 % Allowed : 18.55 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1108 helix: 1.38 (0.27), residues: 391 sheet: -0.26 (0.31), residues: 265 loop : -1.07 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS R 124 PHE 0.026 0.002 PHE H 239 TYR 0.017 0.002 TYR A 230 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 16 ILE cc_start: 0.8673 (mm) cc_final: 0.8256 (mm) REVERT: R 44 GLN cc_start: 0.8297 (mt0) cc_final: 0.7941 (mp10) REVERT: R 107 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8946 (t70) REVERT: R 173 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7074 (mtp-110) REVERT: R 264 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7457 (tp) REVERT: A 247 MET cc_start: 0.6335 (ptt) cc_final: 0.6069 (ptm) REVERT: A 255 ASN cc_start: 0.7937 (m-40) cc_final: 0.7642 (m-40) REVERT: B 142 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.6978 (m90) outliers start: 41 outliers final: 29 residues processed: 197 average time/residue: 0.1907 time to fit residues: 52.5027 Evaluate side-chains 186 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS A 52 GLN A 255 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8936 Z= 0.285 Angle : 0.628 11.090 12117 Z= 0.316 Chirality : 0.044 0.194 1402 Planarity : 0.004 0.049 1507 Dihedral : 4.981 76.919 1240 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.90 % Allowed : 19.94 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1108 helix: 1.40 (0.27), residues: 389 sheet: -0.27 (0.32), residues: 257 loop : -1.01 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 47 HIS 0.005 0.001 HIS R 124 PHE 0.038 0.002 PHE R 255 TYR 0.021 0.002 TYR R 15 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7695 (tt) REVERT: R 44 GLN cc_start: 0.8274 (mt0) cc_final: 0.7863 (mp10) REVERT: R 107 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.9014 (t70) REVERT: R 175 ASP cc_start: 0.7403 (p0) cc_final: 0.6912 (p0) REVERT: R 277 MET cc_start: 0.7272 (ttp) cc_final: 0.6443 (tmm) REVERT: B 142 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7571 (m90) REVERT: H 77 ASN cc_start: 0.5980 (t0) cc_final: 0.5769 (t0) outliers start: 46 outliers final: 30 residues processed: 194 average time/residue: 0.1894 time to fit residues: 51.2398 Evaluate side-chains 186 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 150 ASN Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS B 75 GLN B 237 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8936 Z= 0.220 Angle : 0.601 12.062 12117 Z= 0.300 Chirality : 0.043 0.165 1402 Planarity : 0.004 0.049 1507 Dihedral : 4.760 74.348 1240 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.62 % Allowed : 21.32 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1108 helix: 1.51 (0.27), residues: 389 sheet: -0.32 (0.31), residues: 272 loop : -0.94 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.002 PHE R 255 TYR 0.028 0.001 TYR R 265 ARG 0.007 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 32 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7646 (tt) REVERT: R 44 GLN cc_start: 0.8249 (mt0) cc_final: 0.7834 (mp10) REVERT: A 22 ASN cc_start: 0.7778 (m-40) cc_final: 0.7204 (m110) REVERT: B 304 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7418 (ttt180) REVERT: C 27 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4765 (mpt180) REVERT: H 77 ASN cc_start: 0.6132 (t0) cc_final: 0.5899 (t0) outliers start: 34 outliers final: 22 residues processed: 184 average time/residue: 0.1952 time to fit residues: 50.2769 Evaluate side-chains 176 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 194 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS A 52 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.192 Angle : 0.605 12.537 12117 Z= 0.300 Chirality : 0.042 0.170 1402 Planarity : 0.003 0.043 1507 Dihedral : 4.646 72.180 1240 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.20 % Allowed : 21.75 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1108 helix: 1.52 (0.27), residues: 389 sheet: -0.27 (0.31), residues: 280 loop : -0.91 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 47 HIS 0.009 0.001 HIS B 142 PHE 0.021 0.002 PHE H 239 TYR 0.026 0.001 TYR R 265 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: R 32 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7553 (tt) REVERT: R 44 GLN cc_start: 0.8216 (mt0) cc_final: 0.7827 (mp10) REVERT: R 124 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.5844 (t70) REVERT: A 22 ASN cc_start: 0.7787 (m-40) cc_final: 0.7200 (m110) REVERT: C 27 ARG cc_start: 0.5250 (OUTLIER) cc_final: 0.4752 (mpt180) REVERT: H 77 ASN cc_start: 0.6166 (t0) cc_final: 0.5934 (t0) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.1915 time to fit residues: 49.0666 Evaluate side-chains 177 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.7965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.181 Angle : 0.595 13.737 12117 Z= 0.292 Chirality : 0.042 0.160 1402 Planarity : 0.003 0.045 1507 Dihedral : 4.527 70.214 1240 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.05 % Allowed : 21.00 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1108 helix: 1.59 (0.27), residues: 389 sheet: -0.24 (0.31), residues: 281 loop : -0.87 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP H 47 HIS 0.008 0.001 HIS B 142 PHE 0.019 0.001 PHE H 239 TYR 0.020 0.001 TYR R 265 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8158 (mt0) cc_final: 0.7723 (mp10) REVERT: R 124 HIS cc_start: 0.6575 (OUTLIER) cc_final: 0.5879 (t70) REVERT: R 265 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 22 ASN cc_start: 0.7780 (m-40) cc_final: 0.7172 (m110) REVERT: A 247 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6674 (mtm) REVERT: C 27 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4810 (mpt180) REVERT: H 77 ASN cc_start: 0.6229 (t0) cc_final: 0.5999 (t0) REVERT: H 83 MET cc_start: 0.5513 (ppp) cc_final: 0.5268 (ptp) outliers start: 38 outliers final: 26 residues processed: 182 average time/residue: 0.1695 time to fit residues: 43.5711 Evaluate side-chains 184 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8936 Z= 0.186 Angle : 0.604 13.722 12117 Z= 0.296 Chirality : 0.043 0.156 1402 Planarity : 0.003 0.040 1507 Dihedral : 4.506 68.401 1240 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.41 % Allowed : 21.86 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1108 helix: 1.54 (0.27), residues: 390 sheet: -0.12 (0.31), residues: 276 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP H 47 HIS 0.007 0.001 HIS B 142 PHE 0.045 0.002 PHE R 255 TYR 0.020 0.001 TYR R 265 ARG 0.008 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.038 Fit side-chains REVERT: R 124 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.5935 (t70) REVERT: R 265 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7506 (t80) REVERT: A 22 ASN cc_start: 0.7757 (m-40) cc_final: 0.7142 (m110) REVERT: A 247 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: C 27 ARG cc_start: 0.5370 (OUTLIER) cc_final: 0.4853 (mpt180) REVERT: H 77 ASN cc_start: 0.6302 (t0) cc_final: 0.6086 (t0) outliers start: 32 outliers final: 25 residues processed: 171 average time/residue: 0.1910 time to fit residues: 45.8915 Evaluate side-chains 180 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.8190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8936 Z= 0.178 Angle : 0.619 13.589 12117 Z= 0.303 Chirality : 0.043 0.153 1402 Planarity : 0.003 0.043 1507 Dihedral : 4.468 66.406 1240 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.56 % Allowed : 23.45 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1108 helix: 1.57 (0.27), residues: 389 sheet: -0.08 (0.32), residues: 276 loop : -0.96 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP H 47 HIS 0.012 0.001 HIS R 124 PHE 0.043 0.002 PHE R 255 TYR 0.025 0.001 TYR A 296 ARG 0.011 0.001 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 175 ASP cc_start: 0.6961 (p0) cc_final: 0.6638 (p0) REVERT: R 265 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 22 ASN cc_start: 0.7793 (m-40) cc_final: 0.7174 (m110) REVERT: A 247 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: C 27 ARG cc_start: 0.5366 (OUTLIER) cc_final: 0.4839 (mpt180) REVERT: H 77 ASN cc_start: 0.6298 (t0) cc_final: 0.6096 (t0) outliers start: 24 outliers final: 20 residues processed: 158 average time/residue: 0.1884 time to fit residues: 41.6943 Evaluate side-chains 167 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128955 restraints weight = 12680.803| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.91 r_work: 0.3571 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8936 Z= 0.182 Angle : 0.636 15.042 12117 Z= 0.310 Chirality : 0.043 0.161 1402 Planarity : 0.003 0.042 1507 Dihedral : 4.427 64.731 1240 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.77 % Allowed : 23.45 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1108 helix: 1.39 (0.27), residues: 396 sheet: -0.04 (0.32), residues: 276 loop : -0.93 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 47 HIS 0.007 0.001 HIS B 142 PHE 0.041 0.002 PHE R 255 TYR 0.024 0.001 TYR A 296 ARG 0.008 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.69 seconds wall clock time: 42 minutes 51.08 seconds (2571.08 seconds total)