Starting phenix.real_space_refine on Mon Sep 30 09:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/09_2024/7ul7_26594.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/09_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_26594/09_2024/7ul7_26594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/09_2024/7ul7_26594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/09_2024/7ul7_26594.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/09_2024/7ul7_26594.cif" } 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. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.81, per 1000 atoms: 0.56 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.61 Conformation dependent library (CDL) restraints added in 2.1 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: 2.50 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: 5.32 Time building geometry restraints manager: 5.31 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: 0.00 - 2.37: 23787 2.37 - 4.73: 340 4.73 - 7.10: 29 7.10 - 9.46: 3 9.46 - 11.83: 3 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 3.120 nonbonded pdb=" OD1 ASP E 111 " pdb=" N VAL E 112 " model vdw 2.180 3.120 nonbonded pdb=" O ASN C 184 " pdb=" NE2 GLN C 188 " model vdw 2.198 3.120 nonbonded pdb=" OG SER c 332 " pdb=" OE1 GLN c 334 " model vdw 2.205 3.040 nonbonded pdb=" O LEU L 127 " pdb=" NZ LYS L 185 " model vdw 2.210 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.760 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- 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 : 1.963 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: 0.3124 time to fit residues: 214.4990 Evaluate side-chains 445 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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: 0.0020 chunk 161 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 124 optimal weight: 0.0050 chunk 193 optimal weight: 0.6980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 GLN D 90 GLN E 6 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 35 ASN c 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17820 Z= 0.253 Angle : 0.678 9.539 24162 Z= 0.341 Chirality : 0.046 0.270 2781 Planarity : 0.005 0.072 3021 Dihedral : 7.557 57.056 2973 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.78 % Allowed : 10.47 % Favored : 87.76 % 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: -1.10 (0.29), residues: 312 sheet: 0.53 (0.21), residues: 642 loop : -1.01 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 385 HIS 0.010 0.001 HIS G 210 PHE 0.025 0.002 PHE a 261 TYR 0.027 0.002 TYR D 50 ARG 0.007 0.001 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 487 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 453 time to evaluate : 1.757 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 87 LYS cc_start: 0.6588 (mmmt) cc_final: 0.6370 (tppt) REVERT: C 133 MET cc_start: 0.7543 (mmm) cc_final: 0.6729 (tpt) REVERT: C 195 TRP cc_start: 0.7133 (t60) cc_final: 0.6913 (t60) REVERT: D 83 ASP cc_start: 0.7279 (m-30) cc_final: 0.6750 (m-30) REVERT: D 107 GLU cc_start: 0.6432 (pt0) cc_final: 0.5979 (pt0) REVERT: E 83 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7587 (tp-100) REVERT: E 179 VAL cc_start: 0.8359 (p) cc_final: 0.8048 (m) REVERT: A 66 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6509 (tm-30) REVERT: A 103 GLU cc_start: 0.6608 (tt0) cc_final: 0.6346 (tt0) REVERT: L 82 GLU cc_start: 0.7072 (mp0) cc_final: 0.6772 (mp0) REVERT: H 88 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6773 (mmm160) REVERT: H 126 THR cc_start: 0.8286 (t) cc_final: 0.8078 (m) REVERT: H 211 LYS cc_start: 0.8273 (tppt) cc_final: 0.7883 (tppt) REVERT: B 87 LYS cc_start: 0.7041 (tppt) cc_final: 0.6774 (tppt) REVERT: B 88 ASN cc_start: 0.7652 (p0) cc_final: 0.7433 (p0) REVERT: B 165 TYR cc_start: 0.7572 (m-80) cc_final: 0.7348 (m-10) REVERT: B 236 SER cc_start: 0.7366 (t) cc_final: 0.7146 (m) REVERT: F 6 GLN cc_start: 0.6678 (mp10) cc_final: 0.6434 (mp10) REVERT: F 38 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: G 118 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7690 (p) REVERT: b 320 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: a 356 ASP cc_start: 0.7204 (t70) cc_final: 0.6941 (t0) REVERT: a 367 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7645 (ptmt) REVERT: a 392 TYR cc_start: 0.6974 (m-80) cc_final: 0.6627 (m-80) outliers start: 34 outliers final: 20 residues processed: 463 average time/residue: 0.2947 time to fit residues: 202.9407 Evaluate side-chains 458 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 435 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN 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 H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN 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: 2.9990 chunk 60 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 0.2980 chunk 209 optimal weight: 0.0770 chunk 172 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17820 Z= 0.297 Angle : 0.665 9.668 24162 Z= 0.333 Chirality : 0.045 0.292 2781 Planarity : 0.005 0.067 3021 Dihedral : 7.308 59.532 2973 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.62 % Allowed : 13.61 % Favored : 83.78 % 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 (0.18), residues: 2124 helix: -1.17 (0.28), residues: 312 sheet: 0.41 (0.21), residues: 672 loop : -1.04 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 385 HIS 0.009 0.001 HIS G 210 PHE 0.019 0.002 PHE a 261 TYR 0.025 0.002 TYR D 50 ARG 0.007 0.001 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 487 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 437 time to evaluate : 1.720 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: C 87 LYS cc_start: 0.6873 (mmmt) cc_final: 0.6557 (tppt) REVERT: C 133 MET cc_start: 0.7699 (mmm) cc_final: 0.7309 (mmm) REVERT: C 154 CYS cc_start: 0.3129 (OUTLIER) cc_final: 0.2735 (p) REVERT: D 83 ASP cc_start: 0.7353 (m-30) cc_final: 0.6989 (m-30) REVERT: D 107 GLU cc_start: 0.6453 (pt0) cc_final: 0.5968 (pt0) REVERT: E 30 LYS cc_start: 0.7788 (ptmt) cc_final: 0.7308 (ptmm) REVERT: E 83 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7628 (tp-100) REVERT: E 179 VAL cc_start: 0.8334 (p) cc_final: 0.8038 (m) REVERT: E 187 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7564 (t) REVERT: A 66 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 103 GLU cc_start: 0.6666 (tt0) cc_final: 0.6392 (tt0) REVERT: A 213 MET cc_start: 0.7112 (tmm) cc_final: 0.6885 (tmm) REVERT: H 54 ARG cc_start: 0.7712 (ptt180) cc_final: 0.7453 (ptp-170) REVERT: H 83 GLN cc_start: 0.8162 (tp40) cc_final: 0.7954 (tp40) REVERT: H 88 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6839 (mmm160) REVERT: H 211 LYS cc_start: 0.8311 (tppt) cc_final: 0.7895 (tppt) REVERT: B 236 SER cc_start: 0.7355 (t) cc_final: 0.7065 (m) REVERT: F 6 GLN cc_start: 0.6712 (mp10) cc_final: 0.6418 (mp10) REVERT: G 118 THR cc_start: 0.8001 (p) cc_final: 0.7736 (p) REVERT: b 307 GLU cc_start: 0.7701 (tp30) cc_final: 0.7352 (tp30) REVERT: b 320 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: a 356 ASP cc_start: 0.7251 (t70) cc_final: 0.6951 (t0) REVERT: a 392 TYR cc_start: 0.7006 (m-80) cc_final: 0.6749 (m-80) REVERT: a 409 MET cc_start: 0.6371 (mtt) cc_final: 0.6162 (mtt) outliers start: 50 outliers final: 34 residues processed: 451 average time/residue: 0.2949 time to fit residues: 196.0012 Evaluate side-chains 470 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 433 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER 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 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 22 SER 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 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER 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 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET 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 387 ILE Chi-restraints excluded: chain b residue 388 SER 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: 0.6980 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 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 91 HIS E 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS a 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17820 Z= 0.335 Angle : 0.681 9.966 24162 Z= 0.342 Chirality : 0.046 0.305 2781 Planarity : 0.005 0.065 3021 Dihedral : 7.076 59.836 2973 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.45 % Allowed : 15.96 % Favored : 80.59 % 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: -1.01 (0.18), residues: 2124 helix: -1.30 (0.28), residues: 312 sheet: 0.30 (0.21), residues: 678 loop : -1.06 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 385 HIS 0.008 0.001 HIS G 210 PHE 0.030 0.002 PHE a 261 TYR 0.025 0.002 TYR D 50 ARG 0.008 0.001 ARG b 378 *********************** 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 503 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 437 time to evaluate : 1.802 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 133 MET cc_start: 0.7793 (mmm) cc_final: 0.7408 (mmm) REVERT: C 154 CYS cc_start: 0.3191 (OUTLIER) cc_final: 0.2747 (p) REVERT: D 83 ASP cc_start: 0.7398 (m-30) cc_final: 0.6951 (m-30) REVERT: D 107 GLU cc_start: 0.6608 (pt0) cc_final: 0.6085 (pt0) REVERT: E 80 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5986 (pt) REVERT: E 83 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7678 (tp-100) REVERT: E 179 VAL cc_start: 0.8331 (p) cc_final: 0.8014 (m) REVERT: A 66 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6597 (tm-30) REVERT: A 103 GLU cc_start: 0.6703 (tt0) cc_final: 0.6440 (tt0) REVERT: A 213 MET cc_start: 0.7193 (tmm) cc_final: 0.6807 (tmm) REVERT: H 83 GLN cc_start: 0.8185 (tp40) cc_final: 0.7934 (tp-100) REVERT: H 88 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6880 (mmm160) REVERT: H 126 THR cc_start: 0.8291 (t) cc_final: 0.8078 (m) REVERT: H 211 LYS cc_start: 0.8331 (tppt) cc_final: 0.7897 (tppt) REVERT: B 133 MET cc_start: 0.7523 (tpp) cc_final: 0.6733 (tpt) REVERT: B 236 SER cc_start: 0.7436 (t) cc_final: 0.7158 (m) REVERT: G 2 VAL cc_start: 0.8089 (p) cc_final: 0.7803 (p) REVERT: G 118 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7780 (p) REVERT: c 299 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7268 (mtmm) REVERT: b 307 GLU cc_start: 0.7801 (tp30) cc_final: 0.7412 (tp30) REVERT: b 320 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: a 356 ASP cc_start: 0.7246 (t70) cc_final: 0.6937 (t0) REVERT: a 392 TYR cc_start: 0.7086 (m-80) cc_final: 0.6853 (m-80) outliers start: 66 outliers final: 46 residues processed: 457 average time/residue: 0.2867 time to fit residues: 196.0372 Evaluate side-chains 479 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 429 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 89 SER 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 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 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 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 117 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 57 SER 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 283 MET Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 175 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17820 Z= 0.361 Angle : 0.692 10.067 24162 Z= 0.349 Chirality : 0.046 0.305 2781 Planarity : 0.005 0.062 3021 Dihedral : 6.978 58.698 2973 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.08 % Allowed : 17.16 % Favored : 78.75 % 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: -1.30 (0.29), residues: 294 sheet: 0.27 (0.21), residues: 678 loop : -1.14 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 226 HIS 0.008 0.001 HIS E 102 PHE 0.024 0.002 PHE a 261 TYR 0.026 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 509 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 431 time to evaluate : 1.802 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 154 CYS cc_start: 0.3198 (OUTLIER) cc_final: 0.2743 (p) REVERT: D 83 ASP cc_start: 0.7413 (m-30) cc_final: 0.6967 (m-30) REVERT: D 107 GLU cc_start: 0.6579 (pt0) cc_final: 0.6069 (pt0) REVERT: E 18 LEU cc_start: 0.7362 (tp) cc_final: 0.7084 (tp) REVERT: E 80 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6070 (pt) REVERT: E 83 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7686 (tp-100) REVERT: E 179 VAL cc_start: 0.8315 (p) cc_final: 0.7992 (m) REVERT: A 66 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6487 (tm-30) REVERT: A 68 GLN cc_start: 0.7608 (mt0) cc_final: 0.7108 (mt0) REVERT: A 103 GLU cc_start: 0.6655 (tt0) cc_final: 0.6381 (tt0) REVERT: A 213 MET cc_start: 0.7214 (tmm) cc_final: 0.6813 (tmm) REVERT: H 83 GLN cc_start: 0.8151 (tp40) cc_final: 0.7891 (tp-100) REVERT: H 88 ARG cc_start: 0.7277 (mmm160) cc_final: 0.6863 (mmm160) REVERT: H 126 THR cc_start: 0.8313 (t) cc_final: 0.8092 (m) REVERT: H 211 LYS cc_start: 0.8366 (tppt) cc_final: 0.7910 (tppt) REVERT: B 133 MET cc_start: 0.7671 (tpp) cc_final: 0.6875 (tpt) REVERT: B 236 SER cc_start: 0.7440 (t) cc_final: 0.7131 (m) REVERT: G 2 VAL cc_start: 0.8113 (p) cc_final: 0.7825 (p) REVERT: G 118 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7800 (p) REVERT: c 299 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7264 (mtmm) REVERT: b 320 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: b 378 ARG cc_start: 0.5920 (ttt180) cc_final: 0.5546 (ttt180) REVERT: a 356 ASP cc_start: 0.7243 (t70) cc_final: 0.6946 (t0) REVERT: a 392 TYR cc_start: 0.7099 (m-80) cc_final: 0.6868 (m-80) outliers start: 78 outliers final: 66 residues processed: 463 average time/residue: 0.2820 time to fit residues: 195.2941 Evaluate side-chains 497 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 427 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 89 SER 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 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER 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 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 73 THR 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 H residue 110 MET Chi-restraints excluded: chain B residue 94 ILE 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 131 THR 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 57 SER 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 283 MET 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 387 ILE Chi-restraints excluded: chain b residue 388 SER 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: 0.3980 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17820 Z= 0.323 Angle : 0.683 10.953 24162 Z= 0.342 Chirality : 0.046 0.297 2781 Planarity : 0.005 0.062 3021 Dihedral : 6.834 59.355 2973 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.40 % Allowed : 18.32 % Favored : 77.29 % 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: -1.28 (0.29), residues: 294 sheet: 0.22 (0.21), residues: 684 loop : -1.13 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 36 HIS 0.007 0.001 HIS E 102 PHE 0.022 0.002 PHE a 261 TYR 0.027 0.002 TYR a 365 ARG 0.005 0.001 ARG L 144 *********************** 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 517 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 433 time to evaluate : 1.795 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: 0.7683 (mmm) cc_final: 0.6612 (tpt) REVERT: C 154 CYS cc_start: 0.3261 (OUTLIER) cc_final: 0.2796 (p) REVERT: D 83 ASP cc_start: 0.7405 (m-30) cc_final: 0.6951 (m-30) REVERT: D 107 GLU cc_start: 0.6551 (pt0) cc_final: 0.6083 (pt0) REVERT: E 80 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6096 (pt) REVERT: E 83 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7677 (tp-100) REVERT: E 179 VAL cc_start: 0.8294 (p) cc_final: 0.7973 (m) REVERT: A 66 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 68 GLN cc_start: 0.7568 (mt0) cc_final: 0.7062 (mt0) REVERT: A 213 MET cc_start: 0.7215 (tmm) cc_final: 0.6807 (tmm) REVERT: H 88 ARG cc_start: 0.7267 (mmm160) cc_final: 0.6875 (mmm160) REVERT: H 118 THR cc_start: 0.7494 (p) cc_final: 0.7292 (p) REVERT: H 211 LYS cc_start: 0.8377 (tppt) cc_final: 0.7920 (tppt) REVERT: B 87 LYS cc_start: 0.7245 (tppt) cc_final: 0.6974 (tppt) REVERT: B 133 MET cc_start: 0.7734 (tpp) cc_final: 0.6959 (tpt) REVERT: B 236 SER cc_start: 0.7389 (t) cc_final: 0.7057 (m) REVERT: F 6 GLN cc_start: 0.6697 (mp10) cc_final: 0.6425 (mp10) REVERT: F 164 SER cc_start: 0.7838 (m) cc_final: 0.6941 (t) REVERT: F 207 VAL cc_start: 0.5655 (t) cc_final: 0.5196 (p) REVERT: G 2 VAL cc_start: 0.8124 (p) cc_final: 0.7835 (p) REVERT: G 118 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7752 (p) REVERT: c 299 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7264 (mtmm) REVERT: b 320 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: a 356 ASP cc_start: 0.7227 (t70) cc_final: 0.6930 (t0) REVERT: a 392 TYR cc_start: 0.7069 (m-80) cc_final: 0.6859 (m-80) outliers start: 84 outliers final: 70 residues processed: 467 average time/residue: 0.2860 time to fit residues: 201.7553 Evaluate side-chains 502 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 428 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 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 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER 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 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS 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 154 CYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 73 THR 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 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 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 131 THR 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 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 105 SER 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 283 MET 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 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 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: 0.9990 chunk 117 optimal weight: 6.9990 chunk 150 optimal weight: 0.0980 chunk 116 optimal weight: 0.5980 chunk 173 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 205 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 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 E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17820 Z= 0.228 Angle : 0.656 11.292 24162 Z= 0.324 Chirality : 0.045 0.274 2781 Planarity : 0.005 0.059 3021 Dihedral : 6.553 55.487 2973 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.77 % Allowed : 19.31 % Favored : 76.92 % 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: -0.95 (0.18), residues: 2124 helix: -1.03 (0.30), residues: 294 sheet: 0.26 (0.21), residues: 684 loop : -1.06 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 226 HIS 0.005 0.001 HIS G 210 PHE 0.020 0.001 PHE a 261 TYR 0.024 0.001 TYR D 50 ARG 0.004 0.000 ARG E 99 *********************** 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 508 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 436 time to evaluate : 1.800 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: C 133 MET cc_start: 0.7626 (mmm) cc_final: 0.6570 (tpt) REVERT: C 154 CYS cc_start: 0.3253 (OUTLIER) cc_final: 0.2754 (p) REVERT: D 83 ASP cc_start: 0.7376 (m-30) cc_final: 0.7026 (m-30) REVERT: D 107 GLU cc_start: 0.6514 (pt0) cc_final: 0.6052 (pt0) REVERT: E 80 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6084 (pt) REVERT: E 83 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7655 (tp-100) REVERT: E 111 ASP cc_start: 0.6514 (p0) cc_final: 0.6270 (p0) REVERT: E 179 VAL cc_start: 0.8266 (p) cc_final: 0.7944 (m) REVERT: A 66 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 68 GLN cc_start: 0.7573 (mt0) cc_final: 0.7061 (mt0) REVERT: A 213 MET cc_start: 0.7185 (tmm) cc_final: 0.6807 (tmm) REVERT: H 211 LYS cc_start: 0.8339 (tppt) cc_final: 0.7914 (tppt) REVERT: B 87 LYS cc_start: 0.7183 (tppt) cc_final: 0.6939 (tppt) REVERT: B 133 MET cc_start: 0.7728 (tpp) cc_final: 0.7035 (tpt) REVERT: B 236 SER cc_start: 0.7206 (t) cc_final: 0.6915 (m) REVERT: F 164 SER cc_start: 0.7790 (m) cc_final: 0.6941 (t) REVERT: G 2 VAL cc_start: 0.8154 (p) cc_final: 0.7844 (p) REVERT: G 118 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7724 (p) REVERT: c 299 LYS cc_start: 0.7553 (mtmm) cc_final: 0.7260 (mtmm) REVERT: b 320 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: a 356 ASP cc_start: 0.7201 (t70) cc_final: 0.6901 (t0) REVERT: a 392 TYR cc_start: 0.7056 (m-80) cc_final: 0.6830 (m-80) REVERT: a 407 ASP cc_start: 0.5635 (m-30) cc_final: 0.5333 (m-30) outliers start: 72 outliers final: 57 residues processed: 466 average time/residue: 0.2862 time to fit residues: 199.8970 Evaluate side-chains 490 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 429 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 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 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER 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 127 LEU 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 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS 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 H residue 80 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain B residue 94 ILE 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 212 ILE 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 131 THR 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 105 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain c residue 283 MET 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 387 ILE Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.0170 chunk 81 optimal weight: 0.1980 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN E 6 GLN E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17820 Z= 0.248 Angle : 0.665 11.092 24162 Z= 0.329 Chirality : 0.046 0.278 2781 Planarity : 0.005 0.072 3021 Dihedral : 6.521 55.482 2973 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.19 % Allowed : 19.41 % Favored : 76.40 % 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: -0.94 (0.18), residues: 2124 helix: -1.00 (0.30), residues: 294 sheet: 0.25 (0.21), residues: 684 loop : -1.05 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 226 HIS 0.006 0.001 HIS E 102 PHE 0.018 0.001 PHE a 261 TYR 0.023 0.001 TYR D 50 ARG 0.022 0.001 ARG H 88 *********************** 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 503 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 423 time to evaluate : 1.939 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: 0.7663 (mmm) cc_final: 0.6621 (tpt) REVERT: C 154 CYS cc_start: 0.3314 (OUTLIER) cc_final: 0.2821 (p) REVERT: D 83 ASP cc_start: 0.7370 (m-30) cc_final: 0.7013 (m-30) REVERT: D 107 GLU cc_start: 0.6566 (pt0) cc_final: 0.6106 (pt0) REVERT: E 80 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6091 (pt) REVERT: E 83 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7642 (tp-100) REVERT: E 111 ASP cc_start: 0.6511 (p0) cc_final: 0.6308 (p0) REVERT: E 179 VAL cc_start: 0.8261 (p) cc_final: 0.7943 (m) REVERT: A 66 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6600 (tm-30) REVERT: A 68 GLN cc_start: 0.7579 (mt0) cc_final: 0.7063 (mt0) REVERT: A 133 MET cc_start: 0.7729 (tpp) cc_final: 0.6744 (tpp) REVERT: A 213 MET cc_start: 0.7141 (tmm) cc_final: 0.6757 (tmm) REVERT: H 54 ARG cc_start: 0.7717 (ptt180) cc_final: 0.7403 (ptt180) REVERT: H 83 GLN cc_start: 0.8170 (tp40) cc_final: 0.7925 (tp-100) REVERT: H 211 LYS cc_start: 0.8351 (tppt) cc_final: 0.7922 (tppt) REVERT: B 87 LYS cc_start: 0.7211 (tppt) cc_final: 0.6990 (tppt) REVERT: B 236 SER cc_start: 0.7194 (t) cc_final: 0.6928 (m) REVERT: F 164 SER cc_start: 0.7800 (m) cc_final: 0.6880 (t) REVERT: F 209 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6987 (mmtm) REVERT: G 2 VAL cc_start: 0.8114 (p) cc_final: 0.7808 (p) REVERT: G 118 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7718 (p) REVERT: c 299 LYS cc_start: 0.7555 (mtmm) cc_final: 0.7276 (mtmm) REVERT: b 320 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: a 356 ASP cc_start: 0.7211 (t70) cc_final: 0.6897 (t0) REVERT: a 407 ASP cc_start: 0.5463 (m-30) cc_final: 0.5083 (m-30) outliers start: 80 outliers final: 69 residues processed: 458 average time/residue: 0.2823 time to fit residues: 195.0755 Evaluate side-chains 492 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 419 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 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 188 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 22 SER 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 6 GLN Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS 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 154 CYS Chi-restraints excluded: chain L residue 73 THR 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 H residue 110 MET Chi-restraints excluded: chain B residue 94 ILE 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 212 ILE 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 131 THR 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 105 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain c residue 283 MET 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 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 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: 0.5980 chunk 179 optimal weight: 0.8980 chunk 191 optimal weight: 0.3980 chunk 115 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 150 optimal weight: 0.1980 chunk 58 optimal weight: 0.0980 chunk 172 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN a 405 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17820 Z= 0.223 Angle : 0.669 12.399 24162 Z= 0.327 Chirality : 0.045 0.272 2781 Planarity : 0.005 0.069 3021 Dihedral : 6.370 55.564 2973 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.29 % Allowed : 19.47 % 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: -0.89 (0.19), residues: 2124 helix: -0.89 (0.31), residues: 294 sheet: 0.22 (0.21), residues: 687 loop : -0.99 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 226 HIS 0.006 0.001 HIS E 102 PHE 0.018 0.001 PHE a 261 TYR 0.023 0.001 TYR D 50 ARG 0.016 0.001 ARG H 88 *********************** 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 499 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 417 time to evaluate : 1.802 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: 0.7642 (mmm) cc_final: 0.6596 (tpt) REVERT: C 154 CYS cc_start: 0.3315 (OUTLIER) cc_final: 0.2766 (p) REVERT: D 83 ASP cc_start: 0.7364 (m-30) cc_final: 0.7008 (m-30) REVERT: D 107 GLU cc_start: 0.6561 (pt0) cc_final: 0.6095 (pt0) REVERT: E 80 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.6078 (pt) REVERT: E 83 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7731 (tp-100) REVERT: E 179 VAL cc_start: 0.8250 (p) cc_final: 0.7936 (m) REVERT: A 66 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6602 (tm-30) REVERT: A 68 GLN cc_start: 0.7565 (mt0) cc_final: 0.7046 (mt0) REVERT: A 98 ASN cc_start: 0.7905 (t0) cc_final: 0.7399 (t0) REVERT: A 133 MET cc_start: 0.7708 (tpp) cc_final: 0.6818 (tpp) REVERT: A 213 MET cc_start: 0.7128 (tmm) cc_final: 0.6756 (tmm) REVERT: H 83 GLN cc_start: 0.8160 (tp40) cc_final: 0.7918 (tp-100) REVERT: H 211 LYS cc_start: 0.8341 (tppt) cc_final: 0.7917 (tppt) REVERT: B 236 SER cc_start: 0.7045 (t) cc_final: 0.6809 (m) REVERT: F 164 SER cc_start: 0.7787 (m) cc_final: 0.6943 (t) REVERT: F 207 VAL cc_start: 0.5736 (t) cc_final: 0.5324 (p) REVERT: G 2 VAL cc_start: 0.8117 (p) cc_final: 0.7799 (p) REVERT: G 118 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7696 (p) REVERT: c 299 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7275 (mtmm) REVERT: b 320 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: a 356 ASP cc_start: 0.7208 (t70) cc_final: 0.6890 (t0) outliers start: 82 outliers final: 72 residues processed: 453 average time/residue: 0.2807 time to fit residues: 191.3535 Evaluate side-chains 488 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 412 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 85 CYS 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 188 GLN 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 22 SER 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 6 GLN Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS 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 154 CYS Chi-restraints excluded: chain L residue 73 THR 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 H residue 110 MET Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain B residue 94 ILE 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 212 ILE 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 131 THR 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 c residue 283 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 123 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17820 Z= 0.339 Angle : 0.717 11.888 24162 Z= 0.354 Chirality : 0.046 0.293 2781 Planarity : 0.005 0.063 3021 Dihedral : 6.522 55.383 2973 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.92 % Allowed : 19.94 % Favored : 76.14 % 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: -1.09 (0.29), residues: 294 sheet: 0.18 (0.21), residues: 687 loop : -1.05 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 226 HIS 0.018 0.001 HIS E 102 PHE 0.020 0.002 PHE a 398 TYR 0.022 0.002 TYR D 50 ARG 0.014 0.001 ARG H 88 ********************** 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 505 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 430 time to evaluate : 1.854 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: 0.7758 (mmm) cc_final: 0.6793 (tpt) REVERT: C 154 CYS cc_start: 0.3374 (OUTLIER) cc_final: 0.2803 (p) REVERT: D 83 ASP cc_start: 0.7405 (m-30) cc_final: 0.7062 (m-30) REVERT: D 107 GLU cc_start: 0.6556 (pt0) cc_final: 0.6089 (pt0) REVERT: E 71 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.7772 (t) REVERT: E 80 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6103 (pt) REVERT: E 83 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7653 (tp-100) REVERT: E 179 VAL cc_start: 0.8265 (p) cc_final: 0.7944 (m) REVERT: A 66 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 68 GLN cc_start: 0.7589 (mt0) cc_final: 0.7064 (mt0) REVERT: A 98 ASN cc_start: 0.7950 (t0) cc_final: 0.7680 (t0) REVERT: A 133 MET cc_start: 0.7802 (tpp) cc_final: 0.6927 (tpp) REVERT: A 213 MET cc_start: 0.7219 (tmm) cc_final: 0.6866 (tmm) REVERT: H 84 MET cc_start: 0.7092 (mmp) cc_final: 0.6605 (mmp) REVERT: H 211 LYS cc_start: 0.8384 (tppt) cc_final: 0.7926 (tppt) REVERT: B 236 SER cc_start: 0.7282 (t) cc_final: 0.7001 (m) REVERT: F 164 SER cc_start: 0.7849 (m) cc_final: 0.6824 (t) REVERT: F 207 VAL cc_start: 0.5719 (t) cc_final: 0.5212 (p) REVERT: F 209 LYS cc_start: 0.7316 (mmtt) cc_final: 0.7090 (mmtm) REVERT: G 2 VAL cc_start: 0.8106 (p) cc_final: 0.7791 (p) REVERT: G 118 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7736 (p) REVERT: c 299 LYS cc_start: 0.7563 (mtmm) cc_final: 0.7290 (mtmm) REVERT: b 320 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: a 350 MET cc_start: 0.6129 (tpp) cc_final: 0.5724 (tpp) REVERT: a 356 ASP cc_start: 0.7241 (t70) cc_final: 0.6912 (t0) outliers start: 75 outliers final: 67 residues processed: 461 average time/residue: 0.2844 time to fit residues: 196.2674 Evaluate side-chains 497 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 425 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 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 188 GLN 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 22 SER 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 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 70 THR 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 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS 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 154 CYS Chi-restraints excluded: chain L residue 73 THR 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 H residue 110 MET Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain B residue 94 ILE 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 131 THR 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 c residue 283 MET 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 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: 0.1980 chunk 180 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 169 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141505 restraints weight = 29021.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146204 restraints weight = 16311.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149300 restraints weight = 10998.593| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17820 Z= 0.258 Angle : 0.694 11.752 24162 Z= 0.340 Chirality : 0.045 0.282 2781 Planarity : 0.005 0.061 3021 Dihedral : 6.433 55.445 2973 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.87 % Allowed : 20.46 % Favored : 75.67 % 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: -0.94 (0.18), residues: 2124 helix: -1.00 (0.30), residues: 294 sheet: 0.18 (0.21), residues: 687 loop : -1.00 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 226 HIS 0.006 0.001 HIS H 102 PHE 0.017 0.001 PHE a 261 TYR 0.024 0.001 TYR D 50 ARG 0.013 0.001 ARG H 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4250.93 seconds wall clock time: 76 minutes 35.98 seconds (4595.98 seconds total)