Starting phenix.real_space_refine on Fri Jul 19 17:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/07_2024/8wss_37823.cif" } resolution = 3.01 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= 0.000 sd= 0.002 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 67 5.16 5 C 5624 2.51 5 N 1489 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1749 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} 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: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 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: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1720 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 3 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: "L" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 149 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.01, per 1000 atoms: 0.57 Number of scatterers: 8797 At special positions: 0 Unit cell: (86.52, 122.776, 131.016, 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 67 16.00 O 1617 8.00 N 1489 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.08 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.911A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.623A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.108A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.959A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.672A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.944A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 225 removed outlier: 3.761A pdb=" N ASP H 224 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 225 " --> pdb=" O ALA H 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 221 through 225' Processing helix chain 'R' and resid 111 through 138 Processing helix chain 'R' and resid 145 through 173 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 181 through 216 removed outlier: 3.806A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 222 Processing helix chain 'R' and resid 224 through 250 removed outlier: 4.050A pdb=" N VAL R 228 " --> pdb=" O ARG R 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU R 231 " --> pdb=" O SER R 227 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 272 through 286 removed outlier: 4.262A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 303 Processing helix chain 'R' and resid 313 through 348 removed outlier: 3.675A pdb=" N CYS R 337 " --> pdb=" O VAL R 333 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 338 " --> pdb=" O PHE R 334 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 349 through 351 No H-bonds generated for 'chain 'R' and resid 349 through 351' Processing helix chain 'R' and resid 357 through 384 Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 392 removed outlier: 3.677A pdb=" N VAL R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.887A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.556A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.798A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.482A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.580A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.659A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 147 through 149 removed outlier: 3.541A pdb=" N GLU H 247 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP H 177 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 161 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'R' and resid 253 through 254 433 hydrogen bonds defined for protein. 1203 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: 2.45 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2812 1.34 - 1.46: 2220 1.46 - 1.58: 3854 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 8983 Sorted by residual: bond pdb=" N ARG L 11 " pdb=" CA ARG L 11 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.37e-02 5.33e+03 7.13e+00 bond pdb=" N MET R 165 " pdb=" CA MET R 165 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.04e-02 9.25e+03 5.24e+00 bond pdb=" N ASN R 194 " pdb=" CA ASN R 194 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.97e+00 bond pdb=" N SER R 195 " pdb=" CA SER R 195 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.90e+00 bond pdb=" N GLN R 196 " pdb=" CA GLN R 196 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.56e+00 ... (remaining 8978 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.94: 214 106.94 - 113.70: 4995 113.70 - 120.47: 3291 120.47 - 127.23: 3594 127.23 - 133.99: 95 Bond angle restraints: 12189 Sorted by residual: angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" N LEU H 11 " ideal model delta sigma weight residual 114.23 116.73 -2.50 8.80e-01 1.29e+00 8.04e+00 angle pdb=" N THR R 272 " pdb=" CA THR R 272 " pdb=" C THR R 272 " ideal model delta sigma weight residual 113.18 109.75 3.43 1.33e+00 5.65e-01 6.63e+00 angle pdb=" O ASN R 194 " pdb=" C ASN R 194 " pdb=" N SER R 195 " ideal model delta sigma weight residual 122.12 124.64 -2.52 1.06e+00 8.90e-01 5.65e+00 angle pdb=" CA ASN R 194 " pdb=" C ASN R 194 " pdb=" O ASN R 194 " ideal model delta sigma weight residual 120.55 118.05 2.50 1.06e+00 8.90e-01 5.58e+00 angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" O GLY H 10 " ideal model delta sigma weight residual 122.33 120.55 1.78 8.10e-01 1.52e+00 4.80e+00 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 4952 13.91 - 27.82: 242 27.82 - 41.74: 87 41.74 - 55.65: 21 55.65 - 69.56: 2 Dihedral angle restraints: 5304 sinusoidal: 1992 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLN R 196 " pdb=" CB GLN R 196 " pdb=" CG GLN R 196 " pdb=" CD GLN R 196 " ideal model delta sinusoidal sigma weight residual -180.00 -122.57 -57.43 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU R 284 " pdb=" CA LEU R 284 " pdb=" CB LEU R 284 " pdb=" CG LEU R 284 " ideal model delta sinusoidal sigma weight residual -180.00 -125.25 -54.75 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA LYS G 46 " pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " pdb=" CD LYS G 46 " ideal model delta sinusoidal sigma weight residual -180.00 -125.41 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 835 0.024 - 0.049: 318 0.049 - 0.073: 135 0.073 - 0.097: 66 0.097 - 0.121: 51 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA MET R 112 " pdb=" N MET R 112 " pdb=" C MET R 112 " pdb=" CB MET R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 166 " pdb=" N PRO R 166 " pdb=" C PRO R 166 " pdb=" CB PRO R 166 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1402 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 112 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 113 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 14 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO G 55 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.015 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 94 2.65 - 3.21: 7892 3.21 - 3.77: 13415 3.77 - 4.34: 18204 4.34 - 4.90: 30790 Nonbonded interactions: 70395 Sorted by model distance: nonbonded pdb=" OD1 ASP A 229 " pdb=" CD1 LEU A 232 " model vdw 2.082 3.460 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.220 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.241 2.440 nonbonded pdb=" NH1 ARG H 203 " pdb=" OD2 ASP H 224 " model vdw 2.254 2.520 ... (remaining 70390 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: 1.040 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.390 Find NCS groups from input model: 0.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.002 0.037 8983 Z= 0.127 Angle : 0.456 6.082 12189 Z= 0.259 Chirality : 0.038 0.121 1405 Planarity : 0.003 0.049 1532 Dihedral : 9.953 69.560 3157 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 8.53 % Favored : 91.04 % 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: 1.40 (0.26), residues: 1119 helix: 2.57 (0.27), residues: 376 sheet: 1.50 (0.32), residues: 273 loop : -0.85 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.002 0.000 HIS R 179 PHE 0.007 0.001 PHE R 161 TYR 0.010 0.001 TYR R 275 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 244 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7345 (mtm110) REVERT: A 29 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7314 (ttpt) REVERT: A 195 HIS cc_start: 0.7562 (m-70) cc_final: 0.7216 (t70) REVERT: A 252 SER cc_start: 0.8985 (t) cc_final: 0.8691 (m) REVERT: B 79 LEU cc_start: 0.8583 (mp) cc_final: 0.8356 (mt) REVERT: B 239 ASN cc_start: 0.8612 (m-40) cc_final: 0.8336 (m-40) REVERT: H 109 ASP cc_start: 0.8721 (p0) cc_final: 0.8507 (p0) REVERT: H 221 GLU cc_start: 0.7539 (pm20) cc_final: 0.7149 (pt0) REVERT: R 109 ASN cc_start: 0.4767 (p0) cc_final: 0.4100 (m-40) REVERT: R 127 ASN cc_start: 0.5928 (m-40) cc_final: 0.5721 (m-40) REVERT: R 198 THR cc_start: 0.8398 (t) cc_final: 0.8173 (m) REVERT: R 202 ILE cc_start: 0.8040 (mm) cc_final: 0.7795 (mt) REVERT: R 261 VAL cc_start: 0.7207 (m) cc_final: 0.6815 (p) REVERT: R 280 TYR cc_start: 0.6684 (t80) cc_final: 0.6441 (t80) outliers start: 4 outliers final: 1 residues processed: 247 average time/residue: 0.2391 time to fit residues: 78.7804 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN B 183 HIS B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 82 GLN H 143 GLN H 184 GLN R 171 GLN R 281 GLN R 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8983 Z= 0.193 Angle : 0.520 6.147 12189 Z= 0.272 Chirality : 0.042 0.163 1405 Planarity : 0.004 0.047 1532 Dihedral : 3.763 37.081 1231 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 11.83 % Favored : 84.86 % 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: 1.31 (0.26), residues: 1119 helix: 2.63 (0.28), residues: 377 sheet: 1.57 (0.32), residues: 258 loop : -1.04 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.008 0.001 HIS R 170 PHE 0.025 0.002 PHE R 286 TYR 0.012 0.001 TYR R 275 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.080 Fit side-chains REVERT: A 24 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7387 (mtm110) REVERT: A 29 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7311 (ttpt) REVERT: A 33 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 195 HIS cc_start: 0.7699 (m-70) cc_final: 0.7159 (t-170) REVERT: A 273 LEU cc_start: 0.7891 (mm) cc_final: 0.7649 (mm) REVERT: B 221 THR cc_start: 0.8923 (t) cc_final: 0.8599 (m) REVERT: B 268 ASN cc_start: 0.7877 (t0) cc_final: 0.7595 (t0) REVERT: H 23 SER cc_start: 0.8164 (m) cc_final: 0.7915 (t) REVERT: H 221 GLU cc_start: 0.7644 (pm20) cc_final: 0.7438 (pt0) REVERT: R 109 ASN cc_start: 0.4602 (p0) cc_final: 0.4182 (m-40) REVERT: R 112 MET cc_start: 0.5855 (pmm) cc_final: 0.5631 (pmm) REVERT: R 202 ILE cc_start: 0.8133 (mm) cc_final: 0.7907 (mt) REVERT: R 280 TYR cc_start: 0.6831 (t80) cc_final: 0.6575 (t80) REVERT: R 393 LEU cc_start: 0.0319 (OUTLIER) cc_final: -0.0108 (pp) outliers start: 31 outliers final: 18 residues processed: 174 average time/residue: 0.2084 time to fit residues: 49.7177 Evaluate side-chains 149 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8983 Z= 0.206 Angle : 0.521 7.642 12189 Z= 0.271 Chirality : 0.042 0.150 1405 Planarity : 0.004 0.045 1532 Dihedral : 3.929 35.964 1231 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 3.30 % Allowed : 13.75 % Favored : 82.94 % 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: 1.11 (0.26), residues: 1119 helix: 2.43 (0.27), residues: 385 sheet: 1.42 (0.32), residues: 259 loop : -1.17 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE R 286 TYR 0.012 0.001 TYR R 275 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7504 (mtm110) REVERT: A 29 LYS cc_start: 0.7628 (ttmm) cc_final: 0.7330 (ttpt) REVERT: A 195 HIS cc_start: 0.7744 (m-70) cc_final: 0.7114 (t-170) REVERT: A 273 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7601 (mm) REVERT: A 305 CYS cc_start: 0.7767 (t) cc_final: 0.7184 (m) REVERT: B 146 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 221 THR cc_start: 0.8869 (t) cc_final: 0.8581 (m) REVERT: B 268 ASN cc_start: 0.7837 (t0) cc_final: 0.7566 (t0) REVERT: H 193 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8155 (ttp) REVERT: H 221 GLU cc_start: 0.7741 (pm20) cc_final: 0.7453 (pt0) REVERT: R 109 ASN cc_start: 0.4678 (p0) cc_final: 0.4226 (m-40) REVERT: R 132 PHE cc_start: 0.7446 (t80) cc_final: 0.6781 (t80) REVERT: R 165 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7309 (ttt) REVERT: R 280 TYR cc_start: 0.6854 (t80) cc_final: 0.6625 (t80) outliers start: 31 outliers final: 17 residues processed: 157 average time/residue: 0.2199 time to fit residues: 46.9559 Evaluate side-chains 150 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8983 Z= 0.376 Angle : 0.628 9.667 12189 Z= 0.328 Chirality : 0.046 0.185 1405 Planarity : 0.004 0.045 1532 Dihedral : 4.433 19.891 1229 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.62 % Allowed : 14.82 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.25), residues: 1119 helix: 2.14 (0.27), residues: 384 sheet: 1.01 (0.32), residues: 266 loop : -1.41 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.002 HIS R 170 PHE 0.015 0.002 PHE B 234 TYR 0.016 0.002 TYR R 275 ARG 0.004 0.001 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7765 (ttm170) REVERT: A 29 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7428 (ttpt) REVERT: A 195 HIS cc_start: 0.7727 (m-70) cc_final: 0.7134 (t-170) REVERT: A 273 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7706 (mm) REVERT: A 305 CYS cc_start: 0.7823 (t) cc_final: 0.7271 (m) REVERT: B 46 ARG cc_start: 0.8001 (mpt180) cc_final: 0.7743 (mtm-85) REVERT: B 146 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 221 THR cc_start: 0.8881 (t) cc_final: 0.8605 (m) REVERT: H 38 ARG cc_start: 0.8752 (ttp-170) cc_final: 0.8391 (ttm170) REVERT: H 193 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (ttp) REVERT: R 127 ASN cc_start: 0.7173 (m-40) cc_final: 0.6671 (m110) REVERT: R 144 ASN cc_start: 0.5796 (m-40) cc_final: 0.5514 (t0) REVERT: R 183 THR cc_start: 0.6796 (t) cc_final: 0.6578 (t) REVERT: R 185 CYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5859 (t) REVERT: R 187 LEU cc_start: 0.7185 (tt) cc_final: 0.6667 (mt) REVERT: R 280 TYR cc_start: 0.7089 (t80) cc_final: 0.6827 (t80) outliers start: 34 outliers final: 23 residues processed: 156 average time/residue: 0.2227 time to fit residues: 46.9309 Evaluate side-chains 150 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8983 Z= 0.164 Angle : 0.496 6.444 12189 Z= 0.260 Chirality : 0.041 0.188 1405 Planarity : 0.003 0.044 1532 Dihedral : 3.951 19.412 1229 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 3.52 % Allowed : 15.57 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.26), residues: 1119 helix: 2.37 (0.27), residues: 384 sheet: 1.16 (0.32), residues: 263 loop : -1.30 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 PHE 0.011 0.001 PHE A 196 TYR 0.013 0.001 TYR H 191 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.106 Fit side-chains REVERT: A 29 LYS cc_start: 0.7698 (ttmm) cc_final: 0.7401 (ttpt) REVERT: A 195 HIS cc_start: 0.7716 (m-70) cc_final: 0.7108 (t-170) REVERT: A 273 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7683 (mm) REVERT: A 305 CYS cc_start: 0.7808 (t) cc_final: 0.7286 (m) REVERT: B 46 ARG cc_start: 0.8006 (mpt180) cc_final: 0.7741 (mtm-85) REVERT: B 221 THR cc_start: 0.8785 (t) cc_final: 0.8564 (m) REVERT: H 23 SER cc_start: 0.8378 (m) cc_final: 0.8077 (t) REVERT: H 38 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.8257 (ttm170) REVERT: R 127 ASN cc_start: 0.7023 (m-40) cc_final: 0.6559 (m110) REVERT: R 144 ASN cc_start: 0.5873 (m-40) cc_final: 0.5645 (t0) REVERT: R 185 CYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5690 (t) REVERT: R 187 LEU cc_start: 0.7183 (tt) cc_final: 0.6673 (mt) REVERT: R 198 THR cc_start: 0.8618 (t) cc_final: 0.8233 (t) REVERT: R 280 TYR cc_start: 0.6957 (t80) cc_final: 0.6714 (t80) outliers start: 33 outliers final: 17 residues processed: 154 average time/residue: 0.2402 time to fit residues: 49.5150 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8983 Z= 0.179 Angle : 0.495 6.496 12189 Z= 0.260 Chirality : 0.041 0.188 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.881 21.027 1229 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.62 % Allowed : 15.88 % Favored : 80.49 % 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: 0.93 (0.26), residues: 1119 helix: 2.45 (0.27), residues: 383 sheet: 1.03 (0.32), residues: 265 loop : -1.27 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.010 0.001 PHE R 223 TYR 0.012 0.001 TYR H 191 ARG 0.005 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7401 (ttpt) REVERT: A 195 HIS cc_start: 0.7723 (m-70) cc_final: 0.7116 (t-170) REVERT: A 273 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7694 (mm) REVERT: A 305 CYS cc_start: 0.7805 (t) cc_final: 0.7271 (m) REVERT: B 46 ARG cc_start: 0.7992 (mpt180) cc_final: 0.7727 (mtm-85) REVERT: B 221 THR cc_start: 0.8807 (t) cc_final: 0.8571 (m) REVERT: H 23 SER cc_start: 0.8428 (m) cc_final: 0.8163 (t) REVERT: H 38 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8229 (ttm170) REVERT: H 167 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8957 (tt) REVERT: R 127 ASN cc_start: 0.7003 (m-40) cc_final: 0.6518 (m110) REVERT: R 144 ASN cc_start: 0.5831 (m-40) cc_final: 0.5601 (t0) REVERT: R 185 CYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5768 (t) REVERT: R 187 LEU cc_start: 0.7115 (tt) cc_final: 0.6621 (mt) REVERT: R 280 TYR cc_start: 0.6957 (t80) cc_final: 0.6708 (t80) outliers start: 34 outliers final: 21 residues processed: 147 average time/residue: 0.2287 time to fit residues: 45.3610 Evaluate side-chains 144 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8983 Z= 0.194 Angle : 0.514 6.649 12189 Z= 0.269 Chirality : 0.041 0.199 1405 Planarity : 0.004 0.045 1532 Dihedral : 3.923 21.333 1229 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.09 % Allowed : 16.74 % Favored : 80.17 % 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: 0.89 (0.26), residues: 1119 helix: 2.45 (0.27), residues: 382 sheet: 0.98 (0.32), residues: 265 loop : -1.28 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 PHE 0.010 0.001 PHE H 27 TYR 0.011 0.001 TYR R 342 ARG 0.009 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.017 Fit side-chains REVERT: A 29 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7369 (ttpt) REVERT: A 195 HIS cc_start: 0.7731 (m-70) cc_final: 0.7113 (t-170) REVERT: A 198 MET cc_start: 0.8701 (ttm) cc_final: 0.8392 (mtm) REVERT: A 273 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (mm) REVERT: A 305 CYS cc_start: 0.7812 (t) cc_final: 0.7275 (m) REVERT: B 146 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 221 THR cc_start: 0.8817 (t) cc_final: 0.8580 (m) REVERT: H 23 SER cc_start: 0.8424 (m) cc_final: 0.8170 (t) REVERT: H 38 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8225 (ttm170) REVERT: R 144 ASN cc_start: 0.5839 (m-40) cc_final: 0.5611 (t0) REVERT: R 185 CYS cc_start: 0.6313 (OUTLIER) cc_final: 0.5763 (t) REVERT: R 187 LEU cc_start: 0.7121 (tt) cc_final: 0.6616 (mt) REVERT: R 280 TYR cc_start: 0.6978 (t80) cc_final: 0.6730 (t80) outliers start: 29 outliers final: 21 residues processed: 141 average time/residue: 0.2239 time to fit residues: 42.8043 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8983 Z= 0.331 Angle : 0.598 8.799 12189 Z= 0.313 Chirality : 0.044 0.208 1405 Planarity : 0.004 0.045 1532 Dihedral : 4.354 25.064 1229 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 4.05 % Allowed : 15.78 % Favored : 80.17 % 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: 0.55 (0.25), residues: 1119 helix: 2.19 (0.27), residues: 382 sheet: 0.68 (0.32), residues: 273 loop : -1.47 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 170 PHE 0.014 0.002 PHE B 234 TYR 0.013 0.002 TYR R 342 ARG 0.008 0.001 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.067 Fit side-chains REVERT: A 21 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7856 (ttm170) REVERT: A 29 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7395 (ttpt) REVERT: A 195 HIS cc_start: 0.7705 (m-70) cc_final: 0.7012 (t-90) REVERT: A 273 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 305 CYS cc_start: 0.7876 (t) cc_final: 0.7281 (m) REVERT: B 46 ARG cc_start: 0.7997 (mpt180) cc_final: 0.7751 (mtm-85) REVERT: B 146 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 221 THR cc_start: 0.8882 (t) cc_final: 0.8618 (m) REVERT: H 23 SER cc_start: 0.8422 (m) cc_final: 0.8131 (t) REVERT: H 38 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8398 (ttm170) REVERT: L 13 TYR cc_start: 0.7367 (m-80) cc_final: 0.6684 (m-80) REVERT: R 144 ASN cc_start: 0.5792 (m-40) cc_final: 0.5567 (t0) REVERT: R 185 CYS cc_start: 0.6477 (OUTLIER) cc_final: 0.5951 (t) REVERT: R 187 LEU cc_start: 0.7274 (tt) cc_final: 0.6642 (mt) REVERT: R 198 THR cc_start: 0.8699 (t) cc_final: 0.8324 (t) REVERT: R 280 TYR cc_start: 0.7040 (t80) cc_final: 0.6762 (t80) outliers start: 38 outliers final: 25 residues processed: 150 average time/residue: 0.2276 time to fit residues: 46.0824 Evaluate side-chains 148 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.2980 chunk 60 optimal weight: 0.0040 chunk 43 optimal weight: 0.2980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 overall best weight: 0.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8983 Z= 0.127 Angle : 0.483 6.431 12189 Z= 0.252 Chirality : 0.040 0.210 1405 Planarity : 0.003 0.045 1532 Dihedral : 3.777 20.563 1229 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % 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: 0.81 (0.26), residues: 1119 helix: 2.36 (0.27), residues: 384 sheet: 1.00 (0.32), residues: 259 loop : -1.34 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS A 322 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR H 191 ARG 0.007 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.976 Fit side-chains REVERT: A 29 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7346 (ttpt) REVERT: A 195 HIS cc_start: 0.7653 (m-70) cc_final: 0.7085 (t-170) REVERT: A 272 ASP cc_start: 0.7419 (p0) cc_final: 0.7117 (p0) REVERT: A 273 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7725 (mm) REVERT: A 305 CYS cc_start: 0.7892 (t) cc_final: 0.7253 (m) REVERT: B 146 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 221 THR cc_start: 0.8718 (t) cc_final: 0.8482 (m) REVERT: G 48 ASP cc_start: 0.8727 (t0) cc_final: 0.8381 (t0) REVERT: H 19 LYS cc_start: 0.8337 (tptt) cc_final: 0.8088 (tptp) REVERT: H 23 SER cc_start: 0.8396 (m) cc_final: 0.8132 (t) REVERT: H 38 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8195 (ttm170) REVERT: L 13 TYR cc_start: 0.7211 (m-80) cc_final: 0.6585 (m-80) REVERT: R 185 CYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5070 (t) REVERT: R 187 LEU cc_start: 0.7091 (tt) cc_final: 0.6593 (mt) REVERT: R 189 THR cc_start: 0.6900 (m) cc_final: 0.6499 (m) REVERT: R 198 THR cc_start: 0.8633 (t) cc_final: 0.8253 (t) REVERT: R 279 LEU cc_start: 0.7032 (mm) cc_final: 0.6711 (mt) REVERT: R 280 TYR cc_start: 0.6842 (t80) cc_final: 0.6581 (t80) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.2367 time to fit residues: 47.4555 Evaluate side-chains 146 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8983 Z= 0.181 Angle : 0.507 6.366 12189 Z= 0.266 Chirality : 0.041 0.221 1405 Planarity : 0.003 0.047 1532 Dihedral : 3.808 21.038 1229 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 2.24 % Allowed : 17.48 % Favored : 80.28 % 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: 0.86 (0.26), residues: 1119 helix: 2.45 (0.27), residues: 383 sheet: 1.01 (0.32), residues: 259 loop : -1.35 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.009 0.001 PHE H 27 TYR 0.011 0.001 TYR R 342 ARG 0.007 0.000 ARG R 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.009 Fit side-chains REVERT: A 29 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7356 (ttpt) REVERT: A 195 HIS cc_start: 0.7681 (m-70) cc_final: 0.7056 (t-90) REVERT: A 272 ASP cc_start: 0.7309 (p0) cc_final: 0.7013 (p0) REVERT: A 273 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7705 (mm) REVERT: A 305 CYS cc_start: 0.7927 (t) cc_final: 0.7266 (m) REVERT: B 146 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 221 THR cc_start: 0.8803 (t) cc_final: 0.8555 (m) REVERT: H 23 SER cc_start: 0.8449 (m) cc_final: 0.8186 (t) REVERT: H 38 ARG cc_start: 0.8638 (ttp-170) cc_final: 0.8337 (ttm170) REVERT: L 13 TYR cc_start: 0.7268 (m-80) cc_final: 0.6632 (m-80) REVERT: R 185 CYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5185 (t) REVERT: R 187 LEU cc_start: 0.7052 (tt) cc_final: 0.6542 (mt) REVERT: R 189 THR cc_start: 0.6913 (m) cc_final: 0.6499 (m) REVERT: R 198 THR cc_start: 0.8647 (t) cc_final: 0.8273 (t) REVERT: R 279 LEU cc_start: 0.7102 (mm) cc_final: 0.6784 (mt) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.2359 time to fit residues: 43.4457 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 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 = 0.3697 r_free = 0.3697 target = 0.142529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108440 restraints weight = 11083.288| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.89 r_work: 0.3058 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8983 Z= 0.194 Angle : 0.517 6.412 12189 Z= 0.271 Chirality : 0.041 0.222 1405 Planarity : 0.004 0.048 1532 Dihedral : 3.905 21.643 1229 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.40 % Favored : 96.43 % Rotamer: Outliers : 2.45 % Allowed : 17.06 % Favored : 80.49 % 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: 0.83 (0.26), residues: 1119 helix: 2.44 (0.27), residues: 382 sheet: 0.97 (0.32), residues: 259 loop : -1.35 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.009 0.001 PHE H 27 TYR 0.012 0.001 TYR H 191 ARG 0.007 0.000 ARG R 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.01 seconds wall clock time: 41 minutes 6.78 seconds (2466.78 seconds total)