Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 09:55:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/08_2023/7ul7_26594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/08_2023/7ul7_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_26594/08_2023/7ul7_26594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/08_2023/7ul7_26594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/08_2023/7ul7_26594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul7_26594/08_2023/7ul7_26594.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9444 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 10986 2.51 5 N 2922 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 90": "OE1" <-> "OE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "b GLU 307": "OE1" <-> "OE2" Residue "b PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 9.02, per 1000 atoms: 0.52 Number of scatterers: 17439 At special positions: 0 Unit cell: (187.92, 178.848, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3420 8.00 N 2922 7.00 C 10986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 301 " - " ASN A 88 " " NAG A 302 " - " ASN A 108 " " NAG A 303 " - " ASN A 166 " " NAG A 304 " - " ASN A 223 " " NAG A 305 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 223 " " NAG C 301 " - " ASN C 88 " " NAG C 302 " - " ASN C 108 " " NAG C 303 " - " ASN C 166 " " NAG C 304 " - " ASN C 223 " " NAG C 305 " - " ASN C 118 " " NAG I 1 " - " ASN C 78 " " NAG J 1 " - " ASN A 78 " " NAG K 1 " - " ASN B 78 " " NAG M 1 " - " ASN B 88 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 372 " " NAG a 503 " - " ASN a 394 " " NAG b 501 " - " ASN b 372 " " NAG b 502 " - " ASN b 389 " " NAG b 503 " - " ASN b 394 " " NAG c 501 " - " ASN c 372 " " NAG c 502 " - " ASN c 389 " " NAG c 503 " - " ASN c 394 " Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 2.5 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: 2.02 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: 5.82 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5517 1.35 - 1.47: 4696 1.47 - 1.59: 7445 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 17820 Sorted by residual: bond pdb=" C1 NAG a 503 " pdb=" O5 NAG a 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CB PRO E 133 " pdb=" CG PRO E 133 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.93: 350 105.93 - 112.96: 9811 112.96 - 119.99: 5806 119.99 - 127.01: 7985 127.01 - 134.04: 210 Bond angle restraints: 24162 Sorted by residual: angle pdb=" CA PRO D 206 " pdb=" N PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" CB MET C 133 " pdb=" CG MET C 133 " pdb=" SD MET C 133 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA CYS A 154 " pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 87 " pdb=" CG LYS B 87 " pdb=" CD LYS B 87 " ideal model delta sigma weight residual 111.30 117.93 -6.63 2.30e+00 1.89e-01 8.30e+00 ... (remaining 24157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9206 16.14 - 32.27: 918 32.27 - 48.41: 228 48.41 - 64.55: 40 64.55 - 80.69: 18 Dihedral angle restraints: 10410 sinusoidal: 4086 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 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2628 0.097 - 0.193: 143 0.193 - 0.290: 6 0.290 - 0.386: 3 0.386 - 0.483: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG a 503 " pdb=" ND2 ASN a 394 " pdb=" C2 NAG a 503 " pdb=" O5 NAG a 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2778 not shown) Planarity restraints: 3047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " 0.029 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP a 385 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 385 " 0.026 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP b 385 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP b 385 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP b 385 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP b 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 385 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 59 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO F 60 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 3044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 711 2.71 - 3.26: 17124 3.26 - 3.81: 26466 3.81 - 4.35: 31822 4.35 - 4.90: 54359 Nonbonded interactions: 130482 Sorted by model distance: nonbonded pdb=" OD1 ASP G 111 " pdb=" N VAL G 112 " model vdw 2.165 2.520 nonbonded pdb=" OD1 ASP E 111 " pdb=" N VAL E 112 " model vdw 2.180 2.520 nonbonded pdb=" O ASN C 184 " pdb=" NE2 GLN C 188 " model vdw 2.198 2.520 nonbonded pdb=" OG SER c 332 " pdb=" OE1 GLN c 334 " model vdw 2.205 2.440 nonbonded pdb=" O LEU L 127 " pdb=" NZ LYS L 185 " model vdw 2.210 2.520 ... (remaining 130477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 244 or resid 301 through 303)) selection = chain 'B' selection = (chain 'C' and (resid 65 through 244 or resid 301 through 303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 15.970 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 45.410 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.350 ------------------------------------------------------------------------------- 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 : 13.722 80.686 6261 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 % 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 *********************** 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 : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.2964 time to fit residues: 200.1114 Evaluate side-chains 447 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.0370 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 124 optimal weight: 0.0570 chunk 193 optimal weight: 0.6980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 35 ASN c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 17820 Z= 0.215 Angle : 0.646 9.466 24162 Z= 0.322 Chirality : 0.044 0.256 2781 Planarity : 0.005 0.070 3021 Dihedral : 4.706 22.446 2343 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.57 % 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: -0.80 (0.18), residues: 2124 helix: -0.97 (0.29), residues: 312 sheet: 0.50 (0.21), residues: 642 loop : -0.99 (0.18), residues: 1170 *********************** 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 478 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 448 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 456 average time/residue: 0.3017 time to fit residues: 204.5180 Evaluate side-chains 446 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 428 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1509 time to fit residues: 7.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.1980 chunk 209 optimal weight: 0.9980 chunk 172 optimal weight: 0.0270 chunk 192 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS a 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17820 Z= 0.217 Angle : 0.624 9.460 24162 Z= 0.308 Chirality : 0.044 0.281 2781 Planarity : 0.005 0.064 3021 Dihedral : 4.568 21.584 2343 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.47 % 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: -0.71 (0.18), residues: 2124 helix: -0.90 (0.29), residues: 312 sheet: 0.56 (0.21), residues: 642 loop : -0.93 (0.18), residues: 1170 *********************** 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 459 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 431 time to evaluate : 2.053 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 outliers start: 28 outliers final: 16 residues processed: 442 average time/residue: 0.3053 time to fit residues: 200.6885 Evaluate side-chains 437 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 421 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1930 time to fit residues: 7.6692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.5980 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: 1.9990 chunk 205 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN B 123 HIS B 188 GLN B 229 HIS F 38 GLN G 83 GLN c 373 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.1427 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= 0.343 Angle : 0.691 9.844 24162 Z= 0.345 Chirality : 0.046 0.313 2781 Planarity : 0.005 0.063 3021 Dihedral : 4.857 24.252 2343 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 2.56 % 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: -0.99 (0.18), residues: 2124 helix: -1.12 (0.28), residues: 312 sheet: 0.23 (0.21), residues: 678 loop : -1.05 (0.18), residues: 1134 *********************** 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 494 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 445 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 31 residues processed: 461 average time/residue: 0.3053 time to fit residues: 208.9248 Evaluate side-chains 467 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 436 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1665 time to fit residues: 12.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 153 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 175 optimal weight: 0.3980 chunk 142 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN B 229 HIS F 38 GLN G 102 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17820 Z= 0.211 Angle : 0.634 10.263 24162 Z= 0.314 Chirality : 0.044 0.288 2781 Planarity : 0.005 0.052 3021 Dihedral : 4.659 24.581 2343 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2124 helix: -0.86 (0.30), residues: 294 sheet: 0.33 (0.21), residues: 672 loop : -1.03 (0.18), residues: 1158 *********************** 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 464 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 433 time to evaluate : 1.819 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 outliers start: 31 outliers final: 16 residues processed: 444 average time/residue: 0.2910 time to fit residues: 192.6910 Evaluate side-chains 441 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 425 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1847 time to fit residues: 7.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.0030 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS F 38 GLN c 373 HIS c 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 17820 Z= 0.285 Angle : 0.665 10.524 24162 Z= 0.331 Chirality : 0.045 0.303 2781 Planarity : 0.005 0.055 3021 Dihedral : 4.755 23.337 2343 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2124 helix: -0.89 (0.30), residues: 294 sheet: 0.31 (0.21), residues: 672 loop : -1.05 (0.18), residues: 1158 *********************** 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 477 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 438 time to evaluate : 1.904 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 outliers start: 39 outliers final: 23 residues processed: 450 average time/residue: 0.2909 time to fit residues: 195.6308 Evaluate side-chains 458 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 435 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1613 time to fit residues: 9.6910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 117 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 116 optimal weight: 0.4980 chunk 173 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 205 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS B 229 HIS c 373 HIS c 408 ASN ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.1689 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= 0.240 Angle : 0.651 10.804 24162 Z= 0.322 Chirality : 0.044 0.293 2781 Planarity : 0.004 0.057 3021 Dihedral : 4.701 23.683 2343 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2124 helix: -0.81 (0.30), residues: 294 sheet: 0.29 (0.21), residues: 675 loop : -1.02 (0.18), residues: 1155 *********************** 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 463 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 433 time to evaluate : 1.923 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 outliers start: 30 outliers final: 19 residues processed: 442 average time/residue: 0.3204 time to fit residues: 213.8124 Evaluate side-chains 446 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 427 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1920 time to fit residues: 8.8241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.0070 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 161 optimal weight: 0.0980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 35 ASN E 102 HIS A 68 GLN A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS B 229 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 17820 Z= 0.291 Angle : 0.680 10.970 24162 Z= 0.337 Chirality : 0.045 0.300 2781 Planarity : 0.005 0.049 3021 Dihedral : 4.801 23.541 2343 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 1.26 % 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: -0.88 (0.30), residues: 294 sheet: 0.21 (0.21), residues: 681 loop : -1.05 (0.18), residues: 1149 *********************** 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 466 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 442 time to evaluate : 2.148 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 outliers start: 24 outliers final: 16 residues processed: 447 average time/residue: 0.2915 time to fit residues: 194.1703 Evaluate side-chains 457 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 441 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1543 time to fit residues: 7.1721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 115 optimal weight: 0.0970 chunk 83 optimal weight: 0.2980 chunk 150 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 17820 Z= 0.240 Angle : 0.686 12.227 24162 Z= 0.335 Chirality : 0.045 0.291 2781 Planarity : 0.004 0.051 3021 Dihedral : 4.772 23.483 2343 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 1.10 % 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: -0.90 (0.19), residues: 2124 helix: -0.81 (0.30), residues: 294 sheet: 0.22 (0.21), residues: 681 loop : -1.02 (0.18), residues: 1149 *********************** 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 454 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 433 time to evaluate : 1.819 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 outliers start: 21 outliers final: 13 residues processed: 439 average time/residue: 0.2976 time to fit residues: 195.0492 Evaluate side-chains 440 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 427 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2018 time to fit residues: 7.0148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 0.0570 chunk 140 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 17820 Z= 0.347 Angle : 0.743 12.594 24162 Z= 0.365 Chirality : 0.046 0.306 2781 Planarity : 0.005 0.049 3021 Dihedral : 4.967 24.408 2343 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.47 % 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: -1.04 (0.18), residues: 2124 helix: -1.04 (0.30), residues: 294 sheet: 0.17 (0.21), residues: 681 loop : -1.11 (0.18), residues: 1149 ********************** 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 449 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 440 time to evaluate : 1.695 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 outliers start: 9 outliers final: 6 residues processed: 440 average time/residue: 0.2932 time to fit residues: 191.6804 Evaluate side-chains 440 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 434 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1615 time to fit residues: 4.1959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 51 optimal weight: 0.0980 chunk 155 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 169 optimal weight: 0.0770 chunk 70 optimal weight: 0.0270 chunk 173 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** 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 = 0.4238 r_free = 0.4238 target = 0.173148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145090 restraints weight = 29256.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149809 restraints weight = 16343.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152928 restraints weight = 10960.016| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17820 Z= 0.167 Angle : 0.683 13.076 24162 Z= 0.329 Chirality : 0.044 0.268 2781 Planarity : 0.005 0.054 3021 Dihedral : 4.605 23.180 2343 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.52 % 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: -0.78 (0.19), residues: 2124 helix: -0.71 (0.31), residues: 294 sheet: 0.33 (0.21), residues: 675 loop : -0.96 (0.19), residues: 1155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.79 seconds wall clock time: 76 minutes 23.23 seconds (4583.23 seconds total)