Starting phenix.real_space_refine on Sat Apr 6 23:07:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzh_38796/04_2024/8xzh_38796.pdb" } resolution = 2.6 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= 0.002 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5767 2.51 5 N 1532 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 172": "OD1" <-> "OD2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 194": "OE1" <-> "OE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R GLU 238": "OE1" <-> "OE2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "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 197": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 179": "NH1" <-> "NH2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2419 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1743 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2592 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 416 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1773 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Time building chain proxies: 5.07, per 1000 atoms: 0.56 Number of scatterers: 9048 At special positions: 0 Unit cell: (103, 131.016, 117.008, 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 72 16.00 O 1677 8.00 N 1532 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.02 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: 3.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 40.3% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.163A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 4.147A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 161 removed outlier: 3.774A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.913A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.734A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 299 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.710A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.685A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.651A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.251A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.873A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.811A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.618A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.821A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.797A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.622A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.484A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.721A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.933A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.771A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.741A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.705A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.785A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.211A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.201A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.201A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1326 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: 2.66 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2550 1.33 - 1.45: 1829 1.45 - 1.57: 4764 1.57 - 1.69: 0 1.69 - 1.82: 104 Bond restraints: 9247 Sorted by residual: bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.85e+00 bond pdb=" N ILE A 253 " pdb=" CA ILE A 253 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.22e+00 bond pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.29e-02 6.01e+03 8.38e+00 bond pdb=" N THR R 81 " pdb=" CA THR R 81 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.36e+00 bond pdb=" N ILE A 49 " pdb=" CA ILE A 49 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.22: 183 106.22 - 113.24: 5019 113.24 - 120.26: 3478 120.26 - 127.28: 3747 127.28 - 134.30: 107 Bond angle restraints: 12534 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.02 103.47 9.55 1.20e+00 6.94e-01 6.33e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 120.31 127.69 -7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" C LEU R 30 " pdb=" N ILE R 31 " pdb=" CA ILE R 31 " ideal model delta sigma weight residual 120.24 122.87 -2.63 6.30e-01 2.52e+00 1.75e+01 angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 113.38 108.39 4.99 1.23e+00 6.61e-01 1.65e+01 angle pdb=" N LEU A 273 " pdb=" CA LEU A 273 " pdb=" C LEU A 273 " ideal model delta sigma weight residual 111.28 106.87 4.41 1.09e+00 8.42e-01 1.64e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 4953 17.26 - 34.52: 411 34.52 - 51.78: 74 51.78 - 69.05: 20 69.05 - 86.31: 8 Dihedral angle restraints: 5466 sinusoidal: 2104 harmonic: 3362 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 172.92 -79.92 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 0.00 30.75 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CD ARG S 179 " pdb=" NE ARG S 179 " pdb=" CZ ARG S 179 " pdb=" NH1 ARG S 179 " ideal model delta sinusoidal sigma weight residual 0.00 44.78 -44.78 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 955 0.060 - 0.121: 375 0.121 - 0.181: 72 0.181 - 0.241: 15 0.241 - 0.302: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1416 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 179 " -0.767 9.50e-02 1.11e+02 3.44e-01 7.18e+01 pdb=" NE ARG S 179 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG S 179 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG S 179 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG S 179 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 274 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C THR B 274 " -0.040 2.00e-02 2.50e+03 pdb=" O THR B 274 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 275 " 0.014 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 538 2.72 - 3.26: 8629 3.26 - 3.81: 15032 3.81 - 4.35: 19566 4.35 - 4.90: 33280 Nonbonded interactions: 77045 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.171 2.440 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.198 2.520 nonbonded pdb=" O LEU R 108 " pdb=" ND2 ASN R 112 " model vdw 2.225 2.520 nonbonded pdb=" O PHE A 259 " pdb=" NZ LYS A 317 " model vdw 2.243 2.520 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.273 2.520 ... (remaining 77040 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: 0.570 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: 2.860 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.099 9247 Z= 0.806 Angle : 0.971 10.725 12534 Z= 0.592 Chirality : 0.065 0.302 1419 Planarity : 0.010 0.344 1578 Dihedral : 13.619 86.308 3283 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 0.61 % Allowed : 5.30 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.34 (0.23), residues: 1139 helix: -0.92 (0.24), residues: 404 sheet: 0.10 (0.28), residues: 297 loop : -1.41 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 99 HIS 0.009 0.002 HIS B 91 PHE 0.025 0.003 PHE R 78 TYR 0.034 0.003 TYR B 105 ARG 0.014 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.972 Fit side-chains REVERT: A 298 GLU cc_start: 0.7437 (tp30) cc_final: 0.7179 (tp30) REVERT: A 306 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7323 (mm-40) REVERT: A 308 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7149 (mt-10) outliers start: 6 outliers final: 3 residues processed: 191 average time/residue: 1.5094 time to fit residues: 303.7519 Evaluate side-chains 168 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.0060 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN R 289 ASN A 52 GLN A 188 HIS A 204 GLN A 213 HIS A 306 GLN A 322 HIS B 44 GLN B 259 GLN B 340 ASN G 11 GLN G 24 ASN G 59 ASN S 155 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9247 Z= 0.276 Angle : 0.600 6.447 12534 Z= 0.323 Chirality : 0.044 0.138 1419 Planarity : 0.005 0.055 1578 Dihedral : 5.697 54.153 1266 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 10.09 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.05 (0.24), residues: 1139 helix: 0.66 (0.25), residues: 408 sheet: 0.43 (0.29), residues: 290 loop : -0.94 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.002 TYR S 103 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6266 (ppt170) REVERT: R 318 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: R 321 THR cc_start: 0.7916 (m) cc_final: 0.7685 (m) REVERT: A 52 GLN cc_start: 0.5747 (OUTLIER) cc_final: 0.5226 (mp10) REVERT: A 276 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: A 280 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6994 (mmmt) REVERT: A 298 GLU cc_start: 0.7409 (tp30) cc_final: 0.7181 (tp30) outliers start: 27 outliers final: 6 residues processed: 182 average time/residue: 1.4776 time to fit residues: 283.9879 Evaluate side-chains 175 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9247 Z= 0.210 Angle : 0.548 8.735 12534 Z= 0.295 Chirality : 0.042 0.170 1419 Planarity : 0.005 0.057 1578 Dihedral : 5.374 58.755 1266 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 13.15 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.53 (0.24), residues: 1139 helix: 1.47 (0.26), residues: 403 sheet: 0.61 (0.29), residues: 272 loop : -0.79 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.012 0.001 TYR S 103 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7297 (mpt180) cc_final: 0.6230 (ppt170) REVERT: R 242 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7624 (mmtt) REVERT: R 318 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: A 52 GLN cc_start: 0.5679 (OUTLIER) cc_final: 0.5152 (mt0) REVERT: A 201 VAL cc_start: 0.8636 (p) cc_final: 0.8237 (m) REVERT: A 276 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: B 176 GLN cc_start: 0.8886 (mt0) cc_final: 0.8607 (mt0) REVERT: G 21 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6115 (ppp) REVERT: G 47 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7149 (mp0) outliers start: 20 outliers final: 9 residues processed: 184 average time/residue: 1.4355 time to fit residues: 279.5721 Evaluate side-chains 177 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 97 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9247 Z= 0.255 Angle : 0.562 7.621 12534 Z= 0.301 Chirality : 0.043 0.142 1419 Planarity : 0.005 0.058 1578 Dihedral : 5.217 58.320 1262 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.67 % Allowed : 12.95 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.66 (0.24), residues: 1139 helix: 1.71 (0.26), residues: 402 sheet: 0.47 (0.29), residues: 281 loop : -0.71 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.002 PHE B 199 TYR 0.014 0.001 TYR S 103 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6244 (ppt170) REVERT: R 262 MET cc_start: 0.7061 (ttp) cc_final: 0.6856 (mtt) REVERT: R 318 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: A 52 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.5183 (mt0) REVERT: A 201 VAL cc_start: 0.8656 (p) cc_final: 0.8259 (m) REVERT: A 276 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: A 298 GLU cc_start: 0.7390 (tp30) cc_final: 0.7133 (tp30) REVERT: B 322 ASP cc_start: 0.7693 (m-30) cc_final: 0.7339 (m-30) REVERT: G 21 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.6119 (ppp) outliers start: 36 outliers final: 19 residues processed: 181 average time/residue: 1.5118 time to fit residues: 288.8372 Evaluate side-chains 183 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9247 Z= 0.208 Angle : 0.531 6.981 12534 Z= 0.285 Chirality : 0.042 0.126 1419 Planarity : 0.004 0.057 1578 Dihedral : 5.050 55.696 1262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.57 % Allowed : 13.76 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.82 (0.25), residues: 1139 helix: 1.87 (0.26), residues: 403 sheet: 0.62 (0.29), residues: 278 loop : -0.68 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE B 199 TYR 0.012 0.001 TYR S 103 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 262 MET cc_start: 0.7059 (ttp) cc_final: 0.6848 (mtt) REVERT: R 318 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: A 52 GLN cc_start: 0.5704 (OUTLIER) cc_final: 0.5207 (mt0) REVERT: A 201 VAL cc_start: 0.8571 (p) cc_final: 0.8173 (m) REVERT: A 276 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: A 298 GLU cc_start: 0.7394 (tp30) cc_final: 0.7150 (tp30) REVERT: A 350 ASP cc_start: 0.7571 (t70) cc_final: 0.7207 (t0) REVERT: B 137 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.7591 (mmt-90) REVERT: B 322 ASP cc_start: 0.7618 (m-30) cc_final: 0.7264 (m-30) REVERT: G 21 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6123 (ppp) REVERT: G 47 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: S 212 VAL cc_start: 0.8369 (m) cc_final: 0.8146 (t) outliers start: 35 outliers final: 19 residues processed: 184 average time/residue: 1.4732 time to fit residues: 286.3498 Evaluate side-chains 188 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9247 Z= 0.390 Angle : 0.632 7.424 12534 Z= 0.335 Chirality : 0.046 0.141 1419 Planarity : 0.005 0.059 1578 Dihedral : 5.438 59.156 1262 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.77 % Allowed : 13.86 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.63 (0.25), residues: 1139 helix: 1.59 (0.26), residues: 402 sheet: 0.56 (0.28), residues: 296 loop : -0.75 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 279 HIS 0.007 0.001 HIS B 91 PHE 0.020 0.002 PHE B 199 TYR 0.019 0.002 TYR S 103 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 262 MET cc_start: 0.7079 (ttp) cc_final: 0.6870 (mtt) REVERT: R 318 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: A 52 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.5176 (mt0) REVERT: A 276 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6381 (mt-10) REVERT: A 298 GLU cc_start: 0.7444 (tp30) cc_final: 0.7193 (tp30) REVERT: A 308 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 350 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7267 (t0) REVERT: B 322 ASP cc_start: 0.7726 (m-30) cc_final: 0.7366 (m-30) REVERT: G 47 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7117 (mp0) outliers start: 37 outliers final: 19 residues processed: 187 average time/residue: 1.4781 time to fit residues: 292.1248 Evaluate side-chains 191 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9247 Z= 0.198 Angle : 0.528 6.499 12534 Z= 0.283 Chirality : 0.041 0.170 1419 Planarity : 0.004 0.057 1578 Dihedral : 5.090 54.395 1262 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.06 % Allowed : 15.29 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1139 helix: 1.87 (0.26), residues: 403 sheet: 0.64 (0.29), residues: 275 loop : -0.62 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR S 103 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 318 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: A 52 GLN cc_start: 0.5669 (OUTLIER) cc_final: 0.5199 (mt0) REVERT: A 201 VAL cc_start: 0.8516 (p) cc_final: 0.8229 (m) REVERT: A 276 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: A 350 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7181 (t0) REVERT: B 340 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7640 (m-40) outliers start: 30 outliers final: 19 residues processed: 180 average time/residue: 1.4919 time to fit residues: 283.4028 Evaluate side-chains 184 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9247 Z= 0.242 Angle : 0.552 8.216 12534 Z= 0.294 Chirality : 0.042 0.161 1419 Planarity : 0.005 0.057 1578 Dihedral : 5.070 54.628 1262 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.47 % Allowed : 15.49 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1139 helix: 1.89 (0.26), residues: 403 sheet: 0.60 (0.29), residues: 281 loop : -0.57 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.013 0.001 TYR S 103 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 318 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: A 52 GLN cc_start: 0.5693 (OUTLIER) cc_final: 0.5215 (mt0) REVERT: A 201 VAL cc_start: 0.8540 (p) cc_final: 0.8251 (m) REVERT: A 276 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: A 350 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7212 (t0) REVERT: B 322 ASP cc_start: 0.7666 (m-30) cc_final: 0.7315 (m-30) REVERT: G 47 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7270 (mp0) outliers start: 34 outliers final: 19 residues processed: 184 average time/residue: 1.4589 time to fit residues: 283.8895 Evaluate side-chains 184 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.184 Angle : 0.520 7.162 12534 Z= 0.278 Chirality : 0.041 0.146 1419 Planarity : 0.004 0.057 1578 Dihedral : 4.873 50.976 1262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.75 % Allowed : 16.51 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.97 (0.25), residues: 1139 helix: 2.03 (0.27), residues: 403 sheet: 0.65 (0.29), residues: 276 loop : -0.59 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR S 103 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 272 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6396 (mtm) REVERT: R 318 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: A 201 VAL cc_start: 0.8529 (p) cc_final: 0.8221 (m) REVERT: A 276 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6305 (mt-10) REVERT: A 350 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7193 (t0) REVERT: B 322 ASP cc_start: 0.7718 (m-30) cc_final: 0.7331 (m-30) outliers start: 27 outliers final: 17 residues processed: 180 average time/residue: 1.4383 time to fit residues: 273.5818 Evaluate side-chains 182 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.179 Angle : 0.517 6.219 12534 Z= 0.275 Chirality : 0.041 0.143 1419 Planarity : 0.004 0.057 1578 Dihedral : 4.343 22.131 1257 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 16.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.06 (0.25), residues: 1139 helix: 2.07 (0.26), residues: 404 sheet: 0.70 (0.30), residues: 277 loop : -0.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR S 103 ARG 0.010 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 272 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6391 (mtm) REVERT: A 201 VAL cc_start: 0.8449 (p) cc_final: 0.8160 (m) REVERT: A 276 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: A 350 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7187 (t0) REVERT: B 322 ASP cc_start: 0.7736 (m-30) cc_final: 0.7353 (m-30) REVERT: G 47 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7146 (mp0) outliers start: 26 outliers final: 18 residues processed: 175 average time/residue: 1.4908 time to fit residues: 275.0885 Evaluate side-chains 183 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 193 SER Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.0170 chunk 37 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN B 32 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104309 restraints weight = 13233.574| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.09 r_work: 0.3275 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9247 Z= 0.167 Angle : 0.511 6.197 12534 Z= 0.272 Chirality : 0.041 0.141 1419 Planarity : 0.004 0.057 1578 Dihedral : 4.282 22.029 1257 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.65 % Allowed : 16.82 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.09 (0.25), residues: 1139 helix: 2.10 (0.26), residues: 404 sheet: 0.72 (0.30), residues: 277 loop : -0.50 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.009 0.001 TYR S 103 ARG 0.010 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.99 seconds wall clock time: 84 minutes 57.02 seconds (5097.02 seconds total)