Starting phenix.real_space_refine on Tue Feb 20 04:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/02_2024/7ul7_26594.pdb" } resolution = 3.59 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9444 atoms to isotropic. 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 111 5.16 5 C 10986 2.51 5 N 2922 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 90": "OE1" <-> "OE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "b GLU 307": "OE1" <-> "OE2" Residue "b PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17439 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "E" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "A" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "H" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "F" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "G" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "c" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "b" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.32, per 1000 atoms: 0.53 Number of scatterers: 17439 At special positions: 0 Unit cell: (187.92, 178.848, 103.68, 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 111 16.00 O 3420 8.00 N 2922 7.00 C 10986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 301 " - " ASN A 88 " " NAG A 302 " - " ASN A 108 " " NAG A 303 " - " ASN A 166 " " NAG A 304 " - " ASN A 223 " " NAG A 305 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 223 " " NAG C 301 " - " ASN C 88 " " NAG C 302 " - " ASN C 108 " " NAG C 303 " - " ASN C 166 " " NAG C 304 " - " ASN C 223 " " NAG C 305 " - " ASN C 118 " " NAG I 1 " - " ASN C 78 " " NAG J 1 " - " ASN A 78 " " NAG K 1 " - " ASN B 78 " " NAG M 1 " - " ASN B 88 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 372 " " NAG a 503 " - " ASN a 394 " " NAG b 501 " - " ASN b 372 " " NAG b 502 " - " ASN b 389 " " NAG b 503 " - " ASN b 394 " " NAG c 501 " - " ASN c 372 " " NAG c 502 " - " ASN c 389 " " NAG c 503 " - " ASN c 394 " Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.0 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 37 sheets defined 19.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.041A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.505A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.594A pdb=" N GLY C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.709A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 130' Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 214 Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.167A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 4.204A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.675A pdb=" N LEU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.871A pdb=" N LYS L 190 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.633A pdb=" N HIS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.925A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 143 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.673A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.815A pdb=" N LEU F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 4.051A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 189' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 303 removed outlier: 3.621A pdb=" N LYS c 303 " --> pdb=" O CYS c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 324 removed outlier: 3.824A pdb=" N ARG c 323 " --> pdb=" O LYS c 319 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG c 324 " --> pdb=" O GLN c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 5.489A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.987A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET c 358 " --> pdb=" O LEU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 397 No H-bonds generated for 'chain 'c' and resid 395 through 397' Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.964A pdb=" N ALA c 406 " --> pdb=" O ILE c 402 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN c 408 " --> pdb=" O GLN c 404 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 303 removed outlier: 3.714A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS b 303 " --> pdb=" O CYS b 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 303' Processing helix chain 'b' and resid 307 through 325 removed outlier: 3.525A pdb=" N MET b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG b 323 " --> pdb=" O LYS b 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 325 " --> pdb=" O ALA b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 338 Processing helix chain 'b' and resid 339 through 344 removed outlier: 3.708A pdb=" N LEU b 343 " --> pdb=" O ALA b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 removed outlier: 4.153A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 397 No H-bonds generated for 'chain 'b' and resid 395 through 397' Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.892A pdb=" N ALA b 406 " --> pdb=" O ILE b 402 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN b 408 " --> pdb=" O GLN b 404 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE b 410 " --> pdb=" O ALA b 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 284 removed outlier: 3.600A pdb=" N LEU a 284 " --> pdb=" O ARG a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 303 removed outlier: 3.589A pdb=" N GLU a 302 " --> pdb=" O LYS a 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS a 303 " --> pdb=" O CYS a 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 299 through 303' Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.542A pdb=" N LEU a 325 " --> pdb=" O ALA a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 6.095A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 removed outlier: 4.003A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 397 Processing helix chain 'a' and resid 398 through 413 removed outlier: 4.001A pdb=" N ALA a 406 " --> pdb=" O ILE a 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN a 408 " --> pdb=" O GLN a 404 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET a 409 " --> pdb=" O GLN a 405 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE a 410 " --> pdb=" O ALA a 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.740A pdb=" N LYS c 383 " --> pdb=" O TRP c 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.550A pdb=" N CYS C 85 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 101 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.064A pdb=" N CYS D 23 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE D 72 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 116 through 120 removed outlier: 6.120A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 147 through 151 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN E 3 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.861A pdb=" N GLY E 10 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 60 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 130 through 134 removed outlier: 3.806A pdb=" N ASP E 154 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR E 186 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 88 removed outlier: 5.619A pdb=" N SER A 84 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG A 95 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 86 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR A 93 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 88 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.936A pdb=" N CYS L 23 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.686A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.233A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 147 through 151 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.254A pdb=" N GLN H 3 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.592A pdb=" N GLY H 10 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.958A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AC5, first strand: chain 'B' and resid 66 through 71 removed outlier: 4.410A pdb=" N ASN b 364 " --> pdb=" O TRP b 385 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP b 385 " --> pdb=" O ASN b 364 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N SER b 366 " --> pdb=" O LYS b 383 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N LYS b 383 " --> pdb=" O SER b 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.722A pdb=" N VAL B 163 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.450A pdb=" N LEU F 11 " --> pdb=" O GLU F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.508A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 91 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.058A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 146 through 152 removed outlier: 3.979A pdb=" N VAL F 207 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS F 200 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER F 205 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 6 through 8 removed outlier: 3.841A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.921A pdb=" N GLY G 10 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 60 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 134 removed outlier: 4.858A pdb=" N ALA G 147 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 194 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY G 149 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 192 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU G 151 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER G 190 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS G 153 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 188 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 160 through 164 Processing sheet with id=AD7, first strand: chain 'c' and resid 278 through 279 Processing sheet with id=AD8, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'b' and resid 278 through 279 Processing sheet with id=AE1, first strand: chain 'a' and resid 278 through 279 594 hydrogen bonds defined for protein. 1521 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: 5.24 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5517 1.35 - 1.47: 4696 1.47 - 1.59: 7445 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 17820 Sorted by residual: bond pdb=" C1 NAG a 503 " pdb=" O5 NAG a 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CB PRO E 133 " pdb=" CG PRO E 133 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.93: 350 105.93 - 112.96: 9811 112.96 - 119.99: 5806 119.99 - 127.01: 7985 127.01 - 134.04: 210 Bond angle restraints: 24162 Sorted by residual: angle pdb=" CA PRO D 206 " pdb=" N PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" CB MET C 133 " pdb=" CG MET C 133 " pdb=" SD MET C 133 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA CYS A 154 " pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 87 " pdb=" CG LYS B 87 " pdb=" CD LYS B 87 " ideal model delta sigma weight residual 111.30 117.93 -6.63 2.30e+00 1.89e-01 8.30e+00 ... (remaining 24157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9754 16.14 - 32.27: 946 32.27 - 48.41: 254 48.41 - 64.55: 68 64.55 - 80.69: 18 Dihedral angle restraints: 11040 sinusoidal: 4716 harmonic: 6324 Sorted by residual: dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -147.60 61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS b 278 " pdb=" SG CYS b 278 " pdb=" SG CYS b 291 " pdb=" CB CYS b 291 " ideal model delta sinusoidal sigma weight residual -86.00 -27.29 -58.71 1 1.00e+01 1.00e-02 4.61e+01 ... (remaining 11037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2628 0.097 - 0.193: 143 0.193 - 0.290: 6 0.290 - 0.386: 3 0.386 - 0.483: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG a 503 " pdb=" ND2 ASN a 394 " pdb=" C2 NAG a 503 " pdb=" O5 NAG a 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2778 not shown) Planarity restraints: 3047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " 0.029 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP a 385 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 385 " 0.026 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP b 385 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP b 385 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP b 385 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP b 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 385 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 59 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO F 60 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 3044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 711 2.71 - 3.26: 17124 3.26 - 3.81: 26466 3.81 - 4.35: 31822 4.35 - 4.90: 54359 Nonbonded interactions: 130482 Sorted by model distance: nonbonded pdb=" OD1 ASP G 111 " pdb=" N VAL G 112 " model vdw 2.165 2.520 nonbonded pdb=" OD1 ASP E 111 " pdb=" N VAL E 112 " model vdw 2.180 2.520 nonbonded pdb=" O ASN C 184 " pdb=" NE2 GLN C 188 " model vdw 2.198 2.520 nonbonded pdb=" OG SER c 332 " pdb=" OE1 GLN c 334 " model vdw 2.205 2.440 nonbonded pdb=" O LEU L 127 " pdb=" NZ LYS L 185 " model vdw 2.210 2.520 ... (remaining 130477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 244 or resid 301 through 303)) selection = chain 'B' selection = (chain 'C' and (resid 65 through 244 or resid 301 through 303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 group one per residue 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 15.240 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 46.480 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17820 Z= 0.299 Angle : 0.685 11.825 24162 Z= 0.345 Chirality : 0.049 0.483 2781 Planarity : 0.005 0.083 3021 Dihedral : 13.880 80.686 6891 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.00 (0.18), residues: 2124 helix: -1.18 (0.29), residues: 288 sheet: 0.36 (0.21), residues: 663 loop : -1.13 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP a 385 HIS 0.011 0.001 HIS G 210 PHE 0.036 0.002 PHE b 308 TYR 0.017 0.002 TYR G 155 ARG 0.010 0.001 ARG H 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7656 (t0) cc_final: 0.7438 (t0) REVERT: C 102 LEU cc_start: 0.7200 (mm) cc_final: 0.6989 (mp) REVERT: D 83 ASP cc_start: 0.7091 (m-30) cc_final: 0.6829 (m-30) REVERT: E 179 VAL cc_start: 0.8336 (p) cc_final: 0.8022 (m) REVERT: A 66 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 103 GLU cc_start: 0.6635 (tt0) cc_final: 0.6375 (tt0) REVERT: A 221 ILE cc_start: 0.7135 (mp) cc_final: 0.6896 (mp) REVERT: L 174 THR cc_start: 0.7925 (m) cc_final: 0.7680 (m) REVERT: H 126 THR cc_start: 0.8315 (t) cc_final: 0.8103 (m) REVERT: H 211 LYS cc_start: 0.8289 (tppt) cc_final: 0.7898 (tppt) REVERT: B 87 LYS cc_start: 0.7058 (tppt) cc_final: 0.6551 (tppt) REVERT: c 383 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7350 (ptpp) REVERT: b 383 LYS cc_start: 0.7203 (ptpp) cc_final: 0.6968 (ptpp) REVERT: a 283 MET cc_start: 0.6656 (tpt) cc_final: 0.6268 (mmm) REVERT: a 356 ASP cc_start: 0.7186 (t70) cc_final: 0.6952 (t0) REVERT: a 392 TYR cc_start: 0.6966 (m-80) cc_final: 0.6593 (m-80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3196 time to fit residues: 217.4793 Evaluate side-chains 445 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.0370 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 0.0570 chunk 193 optimal weight: 0.4980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 35 ASN c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17820 Z= 0.221 Angle : 0.645 9.379 24162 Z= 0.322 Chirality : 0.045 0.265 2781 Planarity : 0.005 0.070 3021 Dihedral : 7.610 59.985 2973 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.52 % Allowed : 10.78 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.18), residues: 2124 helix: -1.00 (0.29), residues: 312 sheet: 0.48 (0.21), residues: 645 loop : -0.99 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 385 HIS 0.010 0.001 HIS G 210 PHE 0.026 0.001 PHE a 261 TYR 0.023 0.001 TYR D 50 ARG 0.006 0.000 ARG a 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 445 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7458 (mmm) cc_final: 0.6597 (tpt) REVERT: D 83 ASP cc_start: 0.7109 (m-30) cc_final: 0.6787 (m-30) REVERT: E 83 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7550 (tp-100) REVERT: E 179 VAL cc_start: 0.8364 (p) cc_final: 0.8062 (m) REVERT: A 66 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6499 (tm-30) REVERT: A 103 GLU cc_start: 0.6574 (tt0) cc_final: 0.6320 (tt0) REVERT: H 88 ARG cc_start: 0.7220 (mmm160) cc_final: 0.6764 (mmm160) REVERT: H 126 THR cc_start: 0.8277 (t) cc_final: 0.8068 (m) REVERT: H 211 LYS cc_start: 0.8269 (tppt) cc_final: 0.7902 (tppt) REVERT: B 81 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6712 (mtm) REVERT: B 87 LYS cc_start: 0.7003 (tppt) cc_final: 0.6755 (tppt) REVERT: B 133 MET cc_start: 0.7628 (mmm) cc_final: 0.7390 (tpt) REVERT: B 236 SER cc_start: 0.7330 (t) cc_final: 0.7101 (m) REVERT: G 54 ARG cc_start: 0.6666 (ptt90) cc_final: 0.6423 (ptt90) REVERT: G 110 MET cc_start: 0.6634 (mpp) cc_final: 0.6384 (mpp) REVERT: G 118 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7698 (p) REVERT: a 283 MET cc_start: 0.6258 (tpt) cc_final: 0.6017 (mmm) REVERT: a 291 CYS cc_start: 0.2897 (OUTLIER) cc_final: 0.2678 (t) REVERT: a 356 ASP cc_start: 0.7194 (t70) cc_final: 0.6927 (t0) REVERT: a 367 LYS cc_start: 0.7886 (ptmt) cc_final: 0.7630 (ptmt) REVERT: a 392 TYR cc_start: 0.6974 (m-80) cc_final: 0.6612 (m-80) outliers start: 29 outliers final: 20 residues processed: 452 average time/residue: 0.2930 time to fit residues: 196.6563 Evaluate side-chains 457 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 434 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 0.0980 chunk 209 optimal weight: 0.5980 chunk 172 optimal weight: 0.0870 chunk 192 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17820 Z= 0.243 Angle : 0.627 9.584 24162 Z= 0.312 Chirality : 0.044 0.282 2781 Planarity : 0.005 0.064 3021 Dihedral : 7.080 57.834 2973 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.46 % Allowed : 13.03 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.18), residues: 2124 helix: -0.97 (0.29), residues: 312 sheet: 0.37 (0.21), residues: 675 loop : -0.98 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 385 HIS 0.010 0.001 HIS G 210 PHE 0.020 0.002 PHE a 261 TYR 0.022 0.001 TYR D 50 ARG 0.006 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 446 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 LYS cc_start: 0.6794 (mmmt) cc_final: 0.6587 (tppt) REVERT: C 133 MET cc_start: 0.7664 (mmm) cc_final: 0.7298 (mmm) REVERT: C 154 CYS cc_start: 0.2946 (OUTLIER) cc_final: 0.2631 (p) REVERT: D 83 ASP cc_start: 0.7150 (m-30) cc_final: 0.6858 (m-30) REVERT: D 107 GLU cc_start: 0.6368 (pt0) cc_final: 0.5980 (pt0) REVERT: E 30 LYS cc_start: 0.7678 (ptmt) cc_final: 0.7218 (ptmm) REVERT: E 179 VAL cc_start: 0.8340 (p) cc_final: 0.8052 (m) REVERT: A 66 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 103 GLU cc_start: 0.6637 (tt0) cc_final: 0.6374 (tt0) REVERT: A 213 MET cc_start: 0.7061 (tmm) cc_final: 0.6821 (tmm) REVERT: H 88 ARG cc_start: 0.7210 (mmm160) cc_final: 0.6802 (mmm160) REVERT: H 99 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7936 (ttp-170) REVERT: H 126 THR cc_start: 0.8247 (t) cc_final: 0.8043 (m) REVERT: H 211 LYS cc_start: 0.8299 (tppt) cc_final: 0.7901 (tppt) REVERT: B 103 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6797 (mt-10) REVERT: G 3 GLN cc_start: 0.6469 (pp30) cc_final: 0.6061 (pp30) REVERT: G 5 VAL cc_start: 0.7258 (p) cc_final: 0.6895 (m) REVERT: G 118 THR cc_start: 0.8012 (p) cc_final: 0.7729 (p) REVERT: b 307 GLU cc_start: 0.7589 (tp30) cc_final: 0.7305 (tp30) REVERT: b 320 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: a 291 CYS cc_start: 0.2987 (OUTLIER) cc_final: 0.2734 (t) REVERT: a 356 ASP cc_start: 0.7235 (t70) cc_final: 0.6952 (t0) REVERT: a 392 TYR cc_start: 0.7012 (m-80) cc_final: 0.6787 (m-80) outliers start: 47 outliers final: 30 residues processed: 457 average time/residue: 0.3038 time to fit residues: 205.2886 Evaluate side-chains 470 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 437 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 229 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN c 373 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17820 Z= 0.336 Angle : 0.682 9.925 24162 Z= 0.342 Chirality : 0.046 0.305 2781 Planarity : 0.005 0.063 3021 Dihedral : 6.989 57.116 2973 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.04 % Allowed : 15.70 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.00 (0.18), residues: 2124 helix: -1.14 (0.28), residues: 312 sheet: 0.23 (0.21), residues: 681 loop : -1.05 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 385 HIS 0.008 0.001 HIS G 210 PHE 0.032 0.002 PHE a 261 TYR 0.025 0.002 TYR L 50 ARG 0.006 0.001 ARG a 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 447 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 CYS cc_start: 0.2967 (OUTLIER) cc_final: 0.2633 (p) REVERT: D 83 ASP cc_start: 0.7214 (m-30) cc_final: 0.6902 (m-30) REVERT: D 107 GLU cc_start: 0.6418 (pt0) cc_final: 0.6026 (pt0) REVERT: E 30 LYS cc_start: 0.7897 (ptmt) cc_final: 0.7403 (ptmm) REVERT: E 64 VAL cc_start: 0.8491 (m) cc_final: 0.8210 (t) REVERT: E 80 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6147 (pt) REVERT: E 179 VAL cc_start: 0.8327 (p) cc_final: 0.8011 (m) REVERT: A 66 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 103 GLU cc_start: 0.6675 (tt0) cc_final: 0.6413 (tt0) REVERT: A 154 CYS cc_start: 0.3518 (OUTLIER) cc_final: 0.3230 (p) REVERT: A 213 MET cc_start: 0.7170 (tmm) cc_final: 0.6814 (tmm) REVERT: L 174 THR cc_start: 0.7851 (m) cc_final: 0.7631 (m) REVERT: L 194 TYR cc_start: 0.6378 (m-80) cc_final: 0.6013 (m-80) REVERT: H 83 GLN cc_start: 0.8068 (tp40) cc_final: 0.7854 (tp-100) REVERT: H 88 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6915 (mmm160) REVERT: H 99 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7740 (ttp-170) REVERT: H 126 THR cc_start: 0.8295 (t) cc_final: 0.8078 (m) REVERT: H 211 LYS cc_start: 0.8340 (tppt) cc_final: 0.7897 (tppt) REVERT: F 38 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8111 (tp40) REVERT: G 3 GLN cc_start: 0.6597 (pp30) cc_final: 0.6342 (pp30) REVERT: G 54 ARG cc_start: 0.7002 (ptt90) cc_final: 0.6793 (ptt90) REVERT: G 118 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7868 (p) REVERT: c 299 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7245 (mtmm) REVERT: b 307 GLU cc_start: 0.7769 (tp30) cc_final: 0.7434 (tp30) REVERT: b 320 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: b 378 ARG cc_start: 0.5864 (ttt180) cc_final: 0.5610 (ttt180) REVERT: a 291 CYS cc_start: 0.3019 (OUTLIER) cc_final: 0.2751 (t) REVERT: a 356 ASP cc_start: 0.7239 (t70) cc_final: 0.6930 (t0) REVERT: a 392 TYR cc_start: 0.7089 (m-80) cc_final: 0.6875 (m-80) outliers start: 58 outliers final: 41 residues processed: 467 average time/residue: 0.2936 time to fit residues: 203.3749 Evaluate side-chains 490 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 442 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 279 LEU Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17820 Z= 0.368 Angle : 0.692 9.927 24162 Z= 0.348 Chirality : 0.046 0.306 2781 Planarity : 0.005 0.061 3021 Dihedral : 6.931 56.865 2973 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.13 % Allowed : 17.43 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.13 (0.18), residues: 2124 helix: -1.20 (0.29), residues: 294 sheet: 0.10 (0.20), residues: 711 loop : -1.18 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 385 HIS 0.007 0.001 HIS A 91 PHE 0.024 0.002 PHE a 261 TYR 0.027 0.002 TYR a 365 ARG 0.006 0.001 ARG L 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 448 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7715 (mmm) cc_final: 0.6641 (tpt) REVERT: C 154 CYS cc_start: 0.2974 (OUTLIER) cc_final: 0.2624 (p) REVERT: D 83 ASP cc_start: 0.7247 (m-30) cc_final: 0.6939 (m-30) REVERT: D 107 GLU cc_start: 0.6419 (pt0) cc_final: 0.6020 (pt0) REVERT: E 30 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7516 (ptmm) REVERT: E 80 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6144 (pt) REVERT: A 66 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6493 (tm-30) REVERT: A 68 GLN cc_start: 0.7577 (mt0) cc_final: 0.7066 (mt0) REVERT: A 213 MET cc_start: 0.7212 (tmm) cc_final: 0.6815 (tmm) REVERT: L 194 TYR cc_start: 0.6330 (m-80) cc_final: 0.5981 (m-80) REVERT: H 83 GLN cc_start: 0.8102 (tp40) cc_final: 0.7876 (tp-100) REVERT: H 88 ARG cc_start: 0.7271 (mmm160) cc_final: 0.6870 (mmm160) REVERT: H 211 LYS cc_start: 0.8356 (tppt) cc_final: 0.7889 (tppt) REVERT: B 133 MET cc_start: 0.7598 (tpp) cc_final: 0.7221 (tpt) REVERT: F 38 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: F 164 SER cc_start: 0.7854 (m) cc_final: 0.7004 (t) REVERT: G 2 VAL cc_start: 0.8098 (p) cc_final: 0.7838 (p) REVERT: G 3 GLN cc_start: 0.6621 (pp30) cc_final: 0.6390 (pp30) REVERT: G 118 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7886 (p) REVERT: c 283 MET cc_start: 0.6273 (pmm) cc_final: 0.5882 (pmm) REVERT: c 299 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7251 (mtmm) REVERT: b 320 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: b 378 ARG cc_start: 0.5910 (ttt180) cc_final: 0.5670 (ttt180) REVERT: a 291 CYS cc_start: 0.3065 (OUTLIER) cc_final: 0.2788 (t) REVERT: a 356 ASP cc_start: 0.7233 (t70) cc_final: 0.6942 (t0) REVERT: a 392 TYR cc_start: 0.7102 (m-80) cc_final: 0.6870 (m-80) outliers start: 79 outliers final: 62 residues processed: 477 average time/residue: 0.2970 time to fit residues: 211.4076 Evaluate side-chains 512 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 444 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain b residue 410 ILE Chi-restraints excluded: chain a residue 279 LEU Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 336 ILE Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17820 Z= 0.255 Angle : 0.648 10.556 24162 Z= 0.322 Chirality : 0.045 0.284 2781 Planarity : 0.005 0.059 3021 Dihedral : 6.618 57.076 2973 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.72 % Allowed : 18.89 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.98 (0.18), residues: 2124 helix: -0.98 (0.30), residues: 294 sheet: 0.20 (0.21), residues: 678 loop : -1.07 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 98 HIS 0.006 0.001 HIS G 210 PHE 0.021 0.001 PHE a 261 TYR 0.026 0.002 TYR a 365 ARG 0.006 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 437 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7656 (mmm) cc_final: 0.6585 (tpt) REVERT: C 154 CYS cc_start: 0.2922 (OUTLIER) cc_final: 0.2589 (p) REVERT: D 83 ASP cc_start: 0.7255 (m-30) cc_final: 0.6956 (m-30) REVERT: D 107 GLU cc_start: 0.6515 (pt0) cc_final: 0.6071 (pt0) REVERT: E 18 LEU cc_start: 0.7281 (tp) cc_final: 0.7067 (tp) REVERT: E 71 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.7659 (t) REVERT: E 80 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6109 (pt) REVERT: E 179 VAL cc_start: 0.8263 (p) cc_final: 0.7981 (m) REVERT: A 66 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6614 (tm-30) REVERT: A 68 GLN cc_start: 0.7539 (mt0) cc_final: 0.7026 (mt0) REVERT: A 164 GLN cc_start: 0.8096 (pm20) cc_final: 0.7861 (pm20) REVERT: A 213 MET cc_start: 0.7208 (tmm) cc_final: 0.6813 (tmm) REVERT: L 174 THR cc_start: 0.7849 (m) cc_final: 0.7622 (m) REVERT: H 83 GLN cc_start: 0.8075 (tp40) cc_final: 0.7810 (tp-100) REVERT: H 88 ARG cc_start: 0.7229 (mmm160) cc_final: 0.6875 (mmm160) REVERT: H 118 THR cc_start: 0.7734 (p) cc_final: 0.7469 (p) REVERT: H 211 LYS cc_start: 0.8318 (tppt) cc_final: 0.7882 (tppt) REVERT: B 87 LYS cc_start: 0.6982 (tppt) cc_final: 0.6780 (tppt) REVERT: B 133 MET cc_start: 0.7560 (tpp) cc_final: 0.6741 (tpt) REVERT: F 164 SER cc_start: 0.7817 (m) cc_final: 0.7055 (t) REVERT: G 2 VAL cc_start: 0.8104 (p) cc_final: 0.7804 (p) REVERT: G 118 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7863 (p) REVERT: c 299 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7243 (mtmm) REVERT: b 320 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: a 356 ASP cc_start: 0.7215 (t70) cc_final: 0.6921 (t0) REVERT: a 392 TYR cc_start: 0.7081 (m-80) cc_final: 0.6849 (m-80) REVERT: a 407 ASP cc_start: 0.5657 (m-30) cc_final: 0.5357 (m-30) outliers start: 71 outliers final: 54 residues processed: 465 average time/residue: 0.2976 time to fit residues: 207.5149 Evaluate side-chains 491 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 432 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 279 LEU Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 173 optimal weight: 0.4980 chunk 115 optimal weight: 0.1980 chunk 205 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 chunk 125 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17820 Z= 0.220 Angle : 0.632 10.773 24162 Z= 0.313 Chirality : 0.044 0.278 2781 Planarity : 0.004 0.057 3021 Dihedral : 6.398 57.435 2973 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.61 % Allowed : 19.31 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.18), residues: 2124 helix: -0.79 (0.30), residues: 294 sheet: 0.24 (0.21), residues: 678 loop : -1.03 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 226 HIS 0.005 0.001 HIS G 210 PHE 0.020 0.001 PHE a 261 TYR 0.020 0.001 TYR a 365 ARG 0.008 0.001 ARG b 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 433 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7622 (mmm) cc_final: 0.6541 (tpt) REVERT: C 154 CYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2599 (p) REVERT: D 83 ASP cc_start: 0.7234 (m-30) cc_final: 0.6925 (m-30) REVERT: D 107 GLU cc_start: 0.6464 (pt0) cc_final: 0.6049 (pt0) REVERT: E 71 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.7582 (t) REVERT: E 80 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6071 (pt) REVERT: A 66 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6561 (tm-30) REVERT: A 68 GLN cc_start: 0.7530 (mt0) cc_final: 0.7010 (mt0) REVERT: A 133 MET cc_start: 0.7762 (tpp) cc_final: 0.6986 (tpp) REVERT: A 213 MET cc_start: 0.7203 (tmm) cc_final: 0.6812 (tmm) REVERT: H 118 THR cc_start: 0.7691 (p) cc_final: 0.7416 (p) REVERT: H 211 LYS cc_start: 0.8302 (tppt) cc_final: 0.7872 (tppt) REVERT: B 133 MET cc_start: 0.7547 (tpp) cc_final: 0.6655 (tpt) REVERT: F 38 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8094 (tp40) REVERT: F 164 SER cc_start: 0.7849 (m) cc_final: 0.7092 (t) REVERT: G 2 VAL cc_start: 0.7989 (p) cc_final: 0.7693 (p) REVERT: G 118 THR cc_start: 0.8138 (p) cc_final: 0.7831 (p) REVERT: c 299 LYS cc_start: 0.7537 (mtmm) cc_final: 0.7248 (mtmm) REVERT: b 279 LEU cc_start: 0.8303 (mp) cc_final: 0.8102 (tp) REVERT: b 320 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: a 356 ASP cc_start: 0.7214 (t70) cc_final: 0.6912 (t0) REVERT: a 407 ASP cc_start: 0.5600 (m-30) cc_final: 0.5288 (m-30) outliers start: 69 outliers final: 54 residues processed: 465 average time/residue: 0.2963 time to fit residues: 205.6664 Evaluate side-chains 488 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 429 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 139 optimal weight: 0.0020 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17820 Z= 0.326 Angle : 0.691 10.979 24162 Z= 0.344 Chirality : 0.045 0.296 2781 Planarity : 0.005 0.059 3021 Dihedral : 6.566 57.066 2973 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.03 % Allowed : 19.73 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.00 (0.18), residues: 2124 helix: -0.94 (0.30), residues: 294 sheet: 0.18 (0.21), residues: 678 loop : -1.09 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 226 HIS 0.007 0.001 HIS F 39 PHE 0.020 0.002 PHE a 398 TYR 0.021 0.002 TYR L 50 ARG 0.007 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 444 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7748 (mmm) cc_final: 0.6756 (tpt) REVERT: C 154 CYS cc_start: 0.3009 (OUTLIER) cc_final: 0.2597 (p) REVERT: D 83 ASP cc_start: 0.7270 (m-30) cc_final: 0.6972 (m-30) REVERT: D 107 GLU cc_start: 0.6432 (pt0) cc_final: 0.6032 (pt0) REVERT: D 174 THR cc_start: 0.7896 (m) cc_final: 0.7689 (m) REVERT: E 71 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.7761 (t) REVERT: E 80 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6144 (pt) REVERT: E 179 VAL cc_start: 0.8291 (p) cc_final: 0.8007 (m) REVERT: A 66 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6452 (tm-30) REVERT: A 68 GLN cc_start: 0.7552 (mt0) cc_final: 0.7038 (mt0) REVERT: A 74 MET cc_start: 0.7845 (mmm) cc_final: 0.7480 (mmm) REVERT: A 133 MET cc_start: 0.7890 (tpp) cc_final: 0.7132 (tpp) REVERT: A 164 GLN cc_start: 0.7916 (pm20) cc_final: 0.7646 (pm20) REVERT: A 213 MET cc_start: 0.7210 (tmm) cc_final: 0.6827 (tmm) REVERT: L 174 THR cc_start: 0.7880 (m) cc_final: 0.7637 (m) REVERT: H 118 THR cc_start: 0.7769 (p) cc_final: 0.7497 (p) REVERT: H 211 LYS cc_start: 0.8351 (tppt) cc_final: 0.7894 (tppt) REVERT: B 133 MET cc_start: 0.7645 (tpp) cc_final: 0.6825 (tpt) REVERT: F 164 SER cc_start: 0.7916 (m) cc_final: 0.7025 (t) REVERT: G 2 VAL cc_start: 0.8027 (p) cc_final: 0.7729 (p) REVERT: G 118 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7916 (p) REVERT: c 299 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7269 (mtmm) REVERT: b 320 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: a 356 ASP cc_start: 0.7236 (t70) cc_final: 0.6933 (t0) outliers start: 77 outliers final: 67 residues processed: 479 average time/residue: 0.2809 time to fit residues: 202.9730 Evaluate side-chains 513 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 441 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.8980 chunk 196 optimal weight: 0.3980 chunk 179 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 chunk 150 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17820 Z= 0.224 Angle : 0.668 11.751 24162 Z= 0.327 Chirality : 0.044 0.275 2781 Planarity : 0.005 0.060 3021 Dihedral : 6.400 57.301 2973 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.92 % Allowed : 20.25 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.19), residues: 2124 helix: -0.77 (0.30), residues: 294 sheet: 0.17 (0.21), residues: 681 loop : -1.02 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 226 HIS 0.007 0.001 HIS E 102 PHE 0.018 0.001 PHE a 261 TYR 0.019 0.001 TYR D 50 ARG 0.007 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 432 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 LYS cc_start: 0.6467 (tppt) cc_final: 0.6195 (mmmt) REVERT: C 133 MET cc_start: 0.7724 (mmm) cc_final: 0.6592 (tpt) REVERT: C 154 CYS cc_start: 0.2962 (OUTLIER) cc_final: 0.2551 (p) REVERT: D 83 ASP cc_start: 0.7244 (m-30) cc_final: 0.6940 (m-30) REVERT: D 107 GLU cc_start: 0.6456 (pt0) cc_final: 0.6044 (pt0) REVERT: D 174 THR cc_start: 0.7855 (m) cc_final: 0.7637 (m) REVERT: E 71 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.7961 (m) REVERT: E 80 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.6062 (pt) REVERT: E 179 VAL cc_start: 0.8256 (p) cc_final: 0.7974 (m) REVERT: A 66 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 68 GLN cc_start: 0.7519 (mt0) cc_final: 0.6991 (mt0) REVERT: A 74 MET cc_start: 0.7827 (mmm) cc_final: 0.7470 (mmm) REVERT: A 133 MET cc_start: 0.7806 (tpp) cc_final: 0.7014 (tpp) REVERT: A 164 GLN cc_start: 0.7870 (pm20) cc_final: 0.7597 (pm20) REVERT: A 213 MET cc_start: 0.7219 (tmm) cc_final: 0.6806 (tmm) REVERT: L 144 ARG cc_start: 0.6927 (tpt170) cc_final: 0.6479 (tpt170) REVERT: L 174 THR cc_start: 0.7834 (m) cc_final: 0.7601 (m) REVERT: H 80 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6495 (tt) REVERT: H 118 THR cc_start: 0.7700 (p) cc_final: 0.7423 (p) REVERT: H 211 LYS cc_start: 0.8302 (tppt) cc_final: 0.7868 (tppt) REVERT: B 133 MET cc_start: 0.7645 (tpp) cc_final: 0.6831 (tpt) REVERT: F 38 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7951 (tp40) REVERT: F 164 SER cc_start: 0.7865 (m) cc_final: 0.7195 (t) REVERT: G 2 VAL cc_start: 0.8034 (p) cc_final: 0.7718 (p) REVERT: G 118 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7853 (p) REVERT: c 299 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7273 (mtmm) REVERT: c 403 GLU cc_start: 0.5613 (tm-30) cc_final: 0.5284 (tm-30) REVERT: c 413 MET cc_start: 0.7323 (tmm) cc_final: 0.7085 (tmm) REVERT: b 320 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: a 356 ASP cc_start: 0.7214 (t70) cc_final: 0.6898 (t0) outliers start: 75 outliers final: 62 residues processed: 466 average time/residue: 0.2896 time to fit residues: 202.3247 Evaluate side-chains 496 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 427 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 325 LEU Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 212 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17820 Z= 0.376 Angle : 0.722 11.670 24162 Z= 0.359 Chirality : 0.046 0.297 2781 Planarity : 0.005 0.062 3021 Dihedral : 6.625 57.014 2973 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.13 % Allowed : 19.88 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.07 (0.18), residues: 2124 helix: -0.98 (0.30), residues: 294 sheet: 0.10 (0.21), residues: 681 loop : -1.12 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 98 HIS 0.008 0.001 HIS E 102 PHE 0.023 0.002 PHE a 398 TYR 0.022 0.002 TYR L 50 ARG 0.007 0.001 ARG H 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 430 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7885 (mmm) cc_final: 0.6860 (tpt) REVERT: C 154 CYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2609 (p) REVERT: D 83 ASP cc_start: 0.7269 (m-30) cc_final: 0.6974 (m-30) REVERT: D 107 GLU cc_start: 0.6360 (pt0) cc_final: 0.5992 (pt0) REVERT: E 80 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6160 (pt) REVERT: A 66 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6486 (tm-30) REVERT: A 68 GLN cc_start: 0.7556 (mt0) cc_final: 0.7016 (mt0) REVERT: A 133 MET cc_start: 0.7930 (tpp) cc_final: 0.7153 (tpp) REVERT: A 213 MET cc_start: 0.7246 (tmm) cc_final: 0.6854 (tmm) REVERT: L 144 ARG cc_start: 0.7086 (tpt170) cc_final: 0.6729 (tpt170) REVERT: L 174 THR cc_start: 0.7936 (m) cc_final: 0.7688 (m) REVERT: H 118 THR cc_start: 0.7794 (p) cc_final: 0.7521 (p) REVERT: H 211 LYS cc_start: 0.8367 (tppt) cc_final: 0.7900 (tppt) REVERT: B 133 MET cc_start: 0.7689 (tpp) cc_final: 0.7008 (tpt) REVERT: F 164 SER cc_start: 0.7923 (m) cc_final: 0.7224 (t) REVERT: G 2 VAL cc_start: 0.8024 (p) cc_final: 0.7712 (p) REVERT: G 118 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7947 (p) REVERT: c 299 LYS cc_start: 0.7563 (mtmm) cc_final: 0.7276 (mtmm) REVERT: c 413 MET cc_start: 0.7370 (tmm) cc_final: 0.7126 (tmm) REVERT: b 320 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: a 356 ASP cc_start: 0.7234 (t70) cc_final: 0.6936 (t0) outliers start: 79 outliers final: 70 residues processed: 466 average time/residue: 0.2870 time to fit residues: 201.2743 Evaluate side-chains 502 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 428 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 312 LEU Chi-restraints excluded: chain c residue 319 LYS Chi-restraints excluded: chain c residue 325 LEU Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 333 ILE Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 46 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 173 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.170705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142426 restraints weight = 29107.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147116 restraints weight = 16299.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150241 restraints weight = 10945.088| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17820 Z= 0.184 Angle : 0.670 11.952 24162 Z= 0.325 Chirality : 0.044 0.264 2781 Planarity : 0.004 0.060 3021 Dihedral : 6.292 57.451 2973 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 21.56 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.19), residues: 2124 helix: -0.67 (0.31), residues: 294 sheet: 0.15 (0.21), residues: 681 loop : -0.96 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 226 HIS 0.007 0.001 HIS H 102 PHE 0.018 0.001 PHE a 261 TYR 0.015 0.001 TYR D 50 ARG 0.006 0.000 ARG H 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.36 seconds wall clock time: 79 minutes 29.07 seconds (4769.07 seconds total)