Starting phenix.real_space_refine on Wed Apr 10 01:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/04_2024/8sux_40779_updated.pdb" } resolution = 2.93 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= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 90 5.16 5 C 11434 2.51 5 N 3200 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18101 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3032 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2934 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 349} Chain breaks: 2 Chain: "E" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.47, per 1000 atoms: 0.52 Number of scatterers: 18101 At special positions: 0 Unit cell: (129.92, 116.48, 136.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 12 15.00 O 3365 8.00 N 3200 7.00 C 11434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.1 seconds 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 25 sheets defined 37.5% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 Proline residue: A 49 - end of helix removed outlier: 3.722A pdb=" N GLY A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 119 through 135 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.703A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 193 through 216 Processing helix chain 'A' and resid 226 through 250 removed outlier: 4.249A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.688A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 356 through 359 removed outlier: 4.516A pdb=" N THR A 359 " --> pdb=" O VAL A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 36 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.728A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.769A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 193 through 216 Processing helix chain 'B' and resid 225 through 246 removed outlier: 3.971A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 282 through 301 removed outlier: 3.708A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 4.284A pdb=" N GLN B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE B 335 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 45 Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.946A pdb=" N GLY C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.562A pdb=" N TYR C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 119 through 136 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 194 through 216 removed outlier: 3.734A pdb=" N TRP C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 225 through 250 removed outlier: 4.052A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 282 through 301 removed outlier: 4.096A pdb=" N ARG C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 37 through 52 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.725A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 119 through 136 Processing helix chain 'D' and resid 176 through 183 removed outlier: 4.031A pdb=" N GLY D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 216 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 282 through 301 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.728A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 119 through 136 Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 193 through 215 removed outlier: 4.184A pdb=" N LEU E 215 " --> pdb=" O GLN E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 246 removed outlier: 4.622A pdb=" N LEU E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY E 225 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA E 234 " --> pdb=" O MET E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 282 through 301 removed outlier: 3.836A pdb=" N ARG E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 No H-bonds generated for 'chain 'E' and resid 328 through 331' Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.578A pdb=" N SER E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 358' Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'F' and resid 37 through 46 Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.554A pdb=" N GLY F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE F 54 " --> pdb=" O PHE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 119 through 135 Processing helix chain 'F' and resid 176 through 181 Processing helix chain 'F' and resid 193 through 216 Processing helix chain 'F' and resid 226 through 246 removed outlier: 4.299A pdb=" N ARG F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 282 through 301 Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.604A pdb=" N SER F 358 " --> pdb=" O GLN F 355 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR F 359 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing sheet with id= A, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.758A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 376 through 379 removed outlier: 8.091A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR A 26 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE A 347 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 28 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 349 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 148 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 318 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 150 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASP A 320 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 152 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 74 through 77 Processing sheet with id= D, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= E, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.843A pdb=" N THR B 94 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 6 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B 92 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU B 8 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS B 90 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 376 through 379 removed outlier: 8.212A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N GLN B 370 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR B 26 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 347 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU B 28 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 349 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 148 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU B 318 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 150 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASP B 320 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 152 " --> pdb=" O ASP B 320 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 74 through 77 Processing sheet with id= H, first strand: chain 'B' and resid 255 through 258 Processing sheet with id= I, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.846A pdb=" N THR C 94 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU C 6 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 92 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU C 8 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 90 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 376 through 379 removed outlier: 8.260A pdb=" N ARG C 366 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 27 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU C 368 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 29 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N GLN C 370 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR C 26 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE C 347 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU C 28 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 349 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 148 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU C 318 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C 150 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASP C 320 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 152 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 73 through 75 removed outlier: 4.437A pdb=" N ARG C 73 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 84 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 256 through 258 removed outlier: 3.852A pdb=" N SER C 258 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 264 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.566A pdb=" N GLY D 95 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 103 " --> pdb=" O GLY D 95 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 25 through 28 removed outlier: 8.410A pdb=" N THR D 26 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE D 347 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU D 28 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL D 349 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU D 148 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU D 318 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 150 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ASP D 320 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 152 " --> pdb=" O ASP D 320 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 74 through 77 Processing sheet with id= P, first strand: chain 'D' and resid 256 through 258 Processing sheet with id= Q, first strand: chain 'D' and resid 367 through 370 Processing sheet with id= R, first strand: chain 'E' and resid 16 through 20 removed outlier: 7.096A pdb=" N THR E 94 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU E 6 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU E 8 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 90 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 376 through 379 removed outlier: 8.301A pdb=" N ARG E 366 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 27 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU E 368 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL E 29 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLN E 370 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N THR E 26 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 347 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU E 28 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL E 349 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU E 148 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 318 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 150 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP E 320 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU E 152 " --> pdb=" O ASP E 320 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.685A pdb=" N ILE E 75 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 84 " --> pdb=" O ILE E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 256 through 258 removed outlier: 4.101A pdb=" N SER E 258 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN E 264 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 273 " --> pdb=" O HIS E 269 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.918A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 377 through 379 removed outlier: 7.950A pdb=" N ARG F 366 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 27 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 368 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL F 29 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR F 26 " --> pdb=" O ILE F 345 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE F 347 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU F 28 " --> pdb=" O PHE F 347 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL F 349 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU F 148 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU F 318 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU F 150 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP F 320 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU F 152 " --> pdb=" O ASP F 320 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 74 through 76 Processing sheet with id= Y, first strand: chain 'F' and resid 256 through 258 650 hydrogen bonds defined for protein. 1764 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: 5.93 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5995 1.34 - 1.46: 3260 1.46 - 1.57: 9049 1.57 - 1.69: 20 1.69 - 1.81: 156 Bond restraints: 18480 Sorted by residual: bond pdb=" CB ARG A 285 " pdb=" CG ARG A 285 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB VAL C 291 " pdb=" CG2 VAL C 291 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" CA GLN F 78 " pdb=" CB GLN F 78 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.69e-01 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.40e-01 bond pdb=" CB PRO D 88 " pdb=" CG PRO D 88 " ideal model delta sigma weight residual 1.506 1.538 -0.032 3.90e-02 6.57e+02 6.61e-01 ... (remaining 18475 not shown) Histogram of bond angle deviations from ideal: 99.48 - 107.57: 759 107.57 - 115.66: 11339 115.66 - 123.75: 12336 123.75 - 131.84: 541 131.84 - 139.93: 66 Bond angle restraints: 25041 Sorted by residual: angle pdb=" C LEU E 305 " pdb=" N GLN E 306 " pdb=" CA GLN E 306 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" CA LEU A 124 " pdb=" CB LEU A 124 " pdb=" CG LEU A 124 " ideal model delta sigma weight residual 116.30 129.00 -12.70 3.50e+00 8.16e-02 1.32e+01 angle pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C ARG F 77 " pdb=" N GLN F 78 " pdb=" CA GLN F 78 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C LEU F 305 " pdb=" N GLN F 306 " pdb=" CA GLN F 306 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 ... (remaining 25036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9965 17.92 - 35.85: 1030 35.85 - 53.77: 183 53.77 - 71.69: 59 71.69 - 89.62: 26 Dihedral angle restraints: 11263 sinusoidal: 4721 harmonic: 6542 Sorted by residual: dihedral pdb=" CA LEU E 245 " pdb=" C LEU E 245 " pdb=" N THR E 246 " pdb=" CA THR E 246 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU D 305 " pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR C 246 " pdb=" C THR C 246 " pdb=" N GLN C 247 " pdb=" CA GLN C 247 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1566 0.029 - 0.057: 771 0.057 - 0.086: 276 0.086 - 0.115: 122 0.115 - 0.143: 34 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE E 91 " pdb=" N ILE E 91 " pdb=" C ILE E 91 " pdb=" CB ILE E 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL C 266 " pdb=" N VAL C 266 " pdb=" C VAL C 266 " pdb=" CB VAL C 266 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2766 not shown) Planarity restraints: 3195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 327 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 328 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 48 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 49 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 30 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 31 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " -0.028 5.00e-02 4.00e+02 ... (remaining 3192 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 445 2.71 - 3.26: 16987 3.26 - 3.81: 26884 3.81 - 4.35: 34347 4.35 - 4.90: 59881 Nonbonded interactions: 138544 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" O3G ATP B 501 " model vdw 2.166 2.440 nonbonded pdb=" O CYS E 244 " pdb=" OG SER E 337 " model vdw 2.185 2.440 nonbonded pdb=" OG1 THR D 37 " pdb=" O3G ATP D 501 " model vdw 2.194 2.440 nonbonded pdb=" O PRO C 147 " pdb=" OH TYR C 183 " model vdw 2.195 2.440 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 181 " model vdw 2.205 2.440 ... (remaining 138539 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 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'B' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'C' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'D' and resid 1 through 382) selection = (chain 'E' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'F' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 47.550 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.070 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.003 0.034 18480 Z= 0.217 Angle : 0.534 12.705 25041 Z= 0.292 Chirality : 0.042 0.143 2769 Planarity : 0.005 0.051 3195 Dihedral : 15.607 89.617 6999 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.31 (0.17), residues: 2201 helix: 1.08 (0.19), residues: 765 sheet: -0.27 (0.22), residues: 503 loop : -1.22 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 199 HIS 0.006 0.001 HIS E 327 PHE 0.032 0.001 PHE C 296 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.045 Fit side-chains REVERT: A 15 LYS cc_start: 0.8214 (tttt) cc_final: 0.7928 (tttm) REVERT: A 41 ASP cc_start: 0.7138 (m-30) cc_final: 0.6861 (m-30) REVERT: A 57 SER cc_start: 0.7928 (p) cc_final: 0.7575 (m) REVERT: A 59 TYR cc_start: 0.7908 (m-80) cc_final: 0.7486 (m-80) REVERT: A 63 LYS cc_start: 0.7663 (mttm) cc_final: 0.7226 (mtpt) REVERT: A 110 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6626 (ttm170) REVERT: A 129 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 133 LYS cc_start: 0.7446 (ttpp) cc_final: 0.6113 (mmtt) REVERT: A 134 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6911 (mtm-85) REVERT: A 137 GLU cc_start: 0.6876 (tt0) cc_final: 0.6376 (mt-10) REVERT: A 231 MET cc_start: 0.8323 (mtm) cc_final: 0.7927 (mtp) REVERT: A 256 GLU cc_start: 0.8507 (pt0) cc_final: 0.8224 (pt0) REVERT: A 290 MET cc_start: 0.8130 (ttp) cc_final: 0.7860 (ttm) REVERT: A 334 ILE cc_start: 0.8008 (tt) cc_final: 0.7681 (pt) REVERT: A 361 LYS cc_start: 0.8340 (mttm) cc_final: 0.7501 (ptmm) REVERT: A 362 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7848 (ttp80) REVERT: A 377 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6429 (tptp) REVERT: B 1 MET cc_start: 0.5957 (ptp) cc_final: 0.5400 (mtm) REVERT: B 18 ASP cc_start: 0.7731 (m-30) cc_final: 0.7521 (m-30) REVERT: B 70 GLU cc_start: 0.7511 (mp0) cc_final: 0.7063 (mt-10) REVERT: B 110 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6614 (ttm170) REVERT: B 129 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6927 (mt-10) REVERT: B 133 LYS cc_start: 0.7408 (ttmm) cc_final: 0.6255 (mmtt) REVERT: B 154 THR cc_start: 0.8675 (m) cc_final: 0.8465 (p) REVERT: B 236 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6587 (mt0) REVERT: B 256 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6134 (mp0) REVERT: B 262 ASN cc_start: 0.8253 (t0) cc_final: 0.7876 (m-40) REVERT: B 290 MET cc_start: 0.8058 (ttp) cc_final: 0.7798 (ttm) REVERT: B 312 LYS cc_start: 0.7930 (mttm) cc_final: 0.7688 (mttt) REVERT: B 324 MET cc_start: 0.7373 (mtm) cc_final: 0.6366 (mmm) REVERT: B 362 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8007 (ttp80) REVERT: B 373 ASN cc_start: 0.7983 (m-40) cc_final: 0.7697 (m-40) REVERT: C 5 LYS cc_start: 0.7977 (tttp) cc_final: 0.7432 (tptm) REVERT: C 16 GLN cc_start: 0.7819 (tt0) cc_final: 0.7393 (tm130) REVERT: C 23 GLU cc_start: 0.6883 (tt0) cc_final: 0.6519 (tt0) REVERT: C 77 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6404 (mtm-85) REVERT: C 78 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7101 (tp-100) REVERT: C 110 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6696 (mmt180) REVERT: C 145 GLU cc_start: 0.6566 (pm20) cc_final: 0.6296 (pt0) REVERT: C 244 CYS cc_start: 0.7147 (t) cc_final: 0.6535 (m) REVERT: C 361 LYS cc_start: 0.7879 (mttm) cc_final: 0.7446 (ptpp) REVERT: C 377 LYS cc_start: 0.7643 (mtmm) cc_final: 0.6845 (tmtt) REVERT: D 214 GLN cc_start: 0.6932 (tt0) cc_final: 0.6729 (tt0) REVERT: D 233 GLU cc_start: 0.5402 (mt-10) cc_final: 0.4980 (mm-30) REVERT: D 314 GLN cc_start: 0.7924 (mt0) cc_final: 0.7600 (mt0) REVERT: E 5 LYS cc_start: 0.7494 (ptmt) cc_final: 0.6781 (ptpt) REVERT: E 16 GLN cc_start: 0.7990 (pt0) cc_final: 0.7567 (pm20) REVERT: E 75 ILE cc_start: 0.8055 (pt) cc_final: 0.7496 (mp) REVERT: E 77 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6489 (mtm-85) REVERT: E 84 GLU cc_start: 0.7338 (tp30) cc_final: 0.6637 (mm-30) REVERT: E 106 MET cc_start: 0.7704 (ttm) cc_final: 0.7324 (tmm) REVERT: E 112 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6989 (mp0) REVERT: E 312 LYS cc_start: 0.7460 (mmtp) cc_final: 0.6836 (mttp) REVERT: E 324 MET cc_start: 0.8167 (ttp) cc_final: 0.7852 (ttm) REVERT: E 363 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7596 (mp0) REVERT: E 377 LYS cc_start: 0.7385 (mttp) cc_final: 0.6513 (mptt) REVERT: F 4 ASP cc_start: 0.7947 (m-30) cc_final: 0.7642 (m-30) REVERT: F 214 GLN cc_start: 0.6411 (tm-30) cc_final: 0.6105 (tt0) REVERT: F 261 HIS cc_start: 0.7727 (m90) cc_final: 0.5828 (t70) REVERT: F 262 ASN cc_start: 0.7332 (t0) cc_final: 0.6957 (t0) REVERT: F 267 MET cc_start: 0.8641 (mtt) cc_final: 0.8199 (mmt) REVERT: F 278 SER cc_start: 0.8407 (t) cc_final: 0.8054 (p) REVERT: F 323 ASP cc_start: 0.7517 (p0) cc_final: 0.7238 (p0) outliers start: 0 outliers final: 1 residues processed: 405 average time/residue: 1.4509 time to fit residues: 650.4738 Evaluate side-chains 262 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 210 HIS A 236 GLN A 253 HIS ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 263 GLN B 307 ASN B 314 GLN C 352 HIS D 16 GLN D 130 GLN D 253 HIS D 302 ASN D 332 GLN E 130 GLN F 302 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 18480 Z= 0.554 Angle : 0.824 13.348 25041 Z= 0.417 Chirality : 0.052 0.232 2769 Planarity : 0.008 0.113 3195 Dihedral : 9.617 82.192 2549 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 11.29 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.03 (0.17), residues: 2201 helix: 0.18 (0.18), residues: 767 sheet: -0.56 (0.23), residues: 490 loop : -1.41 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 158 HIS 0.013 0.002 HIS B 269 PHE 0.044 0.003 PHE A 296 TYR 0.019 0.003 TYR A 159 ARG 0.016 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 255 time to evaluate : 2.061 Fit side-chains REVERT: A 18 ASP cc_start: 0.7819 (m-30) cc_final: 0.7613 (m-30) REVERT: A 59 TYR cc_start: 0.7953 (m-80) cc_final: 0.7446 (m-80) REVERT: A 63 LYS cc_start: 0.7875 (mttm) cc_final: 0.7386 (mtpt) REVERT: A 110 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6615 (ttm170) REVERT: A 133 LYS cc_start: 0.7551 (ttpp) cc_final: 0.5852 (mmtt) REVERT: A 134 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6820 (mtp180) REVERT: A 248 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8052 (tt0) REVERT: A 256 GLU cc_start: 0.8652 (pt0) cc_final: 0.8368 (pt0) REVERT: A 267 MET cc_start: 0.9184 (mtp) cc_final: 0.8780 (mtm) REVERT: A 334 ILE cc_start: 0.8235 (tt) cc_final: 0.7688 (pt) REVERT: B 18 ASP cc_start: 0.7734 (m-30) cc_final: 0.7481 (m-30) REVERT: B 110 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6677 (ttt180) REVERT: B 129 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 133 LYS cc_start: 0.7264 (ttmm) cc_final: 0.5927 (mmtt) REVERT: B 236 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7092 (mt0) REVERT: B 262 ASN cc_start: 0.8444 (t0) cc_final: 0.7990 (m-40) REVERT: B 324 MET cc_start: 0.7528 (mtm) cc_final: 0.6645 (mmm) REVERT: B 336 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7671 (tp40) REVERT: C 16 GLN cc_start: 0.8073 (tt0) cc_final: 0.7651 (tt0) REVERT: C 77 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6290 (mtm-85) REVERT: C 90 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8099 (mtpt) REVERT: C 110 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.6712 (mtp85) REVERT: C 112 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6675 (mp0) REVERT: C 145 GLU cc_start: 0.6716 (pm20) cc_final: 0.6437 (pt0) REVERT: C 190 THR cc_start: 0.7201 (m) cc_final: 0.6950 (p) REVERT: C 192 ASN cc_start: 0.7031 (p0) cc_final: 0.6743 (p0) REVERT: C 244 CYS cc_start: 0.7517 (t) cc_final: 0.6768 (m) REVERT: C 282 ASP cc_start: 0.7981 (m-30) cc_final: 0.7718 (m-30) REVERT: C 361 LYS cc_start: 0.8017 (mttm) cc_final: 0.7511 (ptpp) REVERT: C 377 LYS cc_start: 0.7746 (mtmm) cc_final: 0.6858 (tmtt) REVERT: D 106 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5859 (tpp) REVERT: D 120 MET cc_start: 0.5501 (tpp) cc_final: 0.5175 (ttt) REVERT: D 192 ASN cc_start: 0.8045 (p0) cc_final: 0.7599 (t0) REVERT: D 262 ASN cc_start: 0.7905 (t0) cc_final: 0.7591 (t0) REVERT: D 271 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: D 355 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: E 77 ARG cc_start: 0.7333 (mtp180) cc_final: 0.6154 (mtm-85) REVERT: E 106 MET cc_start: 0.8172 (ttm) cc_final: 0.7597 (tmm) REVERT: E 112 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6718 (mp0) REVERT: E 127 TRP cc_start: 0.5147 (t60) cc_final: 0.4917 (t60) REVERT: E 300 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6232 (mtmt) REVERT: E 363 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7612 (mp0) REVERT: E 377 LYS cc_start: 0.7502 (mttp) cc_final: 0.6883 (mtmt) REVERT: F 1 MET cc_start: 0.3879 (tpt) cc_final: 0.3653 (tpt) REVERT: F 195 GLN cc_start: 0.7423 (mp10) cc_final: 0.6727 (mt0) REVERT: F 214 GLN cc_start: 0.6561 (tm-30) cc_final: 0.6254 (tt0) REVERT: F 262 ASN cc_start: 0.8119 (t0) cc_final: 0.7719 (t0) REVERT: F 267 MET cc_start: 0.8904 (mtt) cc_final: 0.8539 (mtt) REVERT: F 271 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: F 278 SER cc_start: 0.8686 (t) cc_final: 0.8401 (p) REVERT: F 355 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7274 (mt0) outliers start: 53 outliers final: 19 residues processed: 290 average time/residue: 1.4441 time to fit residues: 465.9673 Evaluate side-chains 260 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 198 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN B 333 GLN C 130 GLN D 16 GLN D 302 ASN D 344 GLN D 375 ASN F 302 ASN F 307 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18480 Z= 0.147 Angle : 0.493 7.106 25041 Z= 0.265 Chirality : 0.040 0.145 2769 Planarity : 0.005 0.048 3195 Dihedral : 8.614 89.062 2547 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.16 % Allowed : 14.89 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.58 (0.17), residues: 2201 helix: 0.66 (0.18), residues: 788 sheet: -0.39 (0.22), residues: 498 loop : -1.23 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 199 HIS 0.010 0.001 HIS C 269 PHE 0.019 0.001 PHE A 296 TYR 0.013 0.001 TYR B 163 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 2.018 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7806 (m-30) cc_final: 0.7577 (m-30) REVERT: A 59 TYR cc_start: 0.7953 (m-80) cc_final: 0.7632 (m-80) REVERT: A 63 LYS cc_start: 0.7859 (mttm) cc_final: 0.7371 (mtpt) REVERT: A 110 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6511 (ttm170) REVERT: A 134 ARG cc_start: 0.6902 (mmm-85) cc_final: 0.6516 (mtp180) REVERT: A 231 MET cc_start: 0.8349 (mtm) cc_final: 0.7693 (mtp) REVERT: A 256 GLU cc_start: 0.8608 (pt0) cc_final: 0.8386 (pt0) REVERT: A 267 MET cc_start: 0.9083 (mtp) cc_final: 0.8780 (mtm) REVERT: B 18 ASP cc_start: 0.7768 (m-30) cc_final: 0.7531 (m-30) REVERT: B 110 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6614 (ttt180) REVERT: B 129 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7009 (mt-10) REVERT: B 133 LYS cc_start: 0.7144 (ttmm) cc_final: 0.5771 (mmtt) REVERT: B 236 GLN cc_start: 0.7724 (tm-30) cc_final: 0.6975 (mt0) REVERT: B 262 ASN cc_start: 0.8402 (t0) cc_final: 0.7993 (m-40) REVERT: B 324 MET cc_start: 0.7315 (mtm) cc_final: 0.6497 (mmm) REVERT: B 336 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7545 (tp40) REVERT: C 5 LYS cc_start: 0.8130 (tttp) cc_final: 0.7715 (tttm) REVERT: C 16 GLN cc_start: 0.8099 (tt0) cc_final: 0.7595 (tm-30) REVERT: C 77 ARG cc_start: 0.7349 (mtt-85) cc_final: 0.6223 (mtm-85) REVERT: C 78 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7243 (tp-100) REVERT: C 108 ASP cc_start: 0.7789 (p0) cc_final: 0.7568 (p0) REVERT: C 110 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6755 (mtp85) REVERT: C 112 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6541 (mp0) REVERT: C 145 GLU cc_start: 0.6743 (pm20) cc_final: 0.6451 (pt0) REVERT: C 190 THR cc_start: 0.7209 (m) cc_final: 0.6974 (p) REVERT: C 361 LYS cc_start: 0.8056 (mttm) cc_final: 0.7514 (mtmm) REVERT: C 377 LYS cc_start: 0.7733 (mtmm) cc_final: 0.6814 (tptt) REVERT: D 4 ASP cc_start: 0.7915 (m-30) cc_final: 0.7550 (m-30) REVERT: D 106 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5695 (tpp) REVERT: D 120 MET cc_start: 0.5491 (tpp) cc_final: 0.5187 (ttt) REVERT: D 267 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8492 (tpp) REVERT: D 271 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: E 77 ARG cc_start: 0.7179 (mtp180) cc_final: 0.5977 (mtm-85) REVERT: E 84 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: E 106 MET cc_start: 0.8127 (ttm) cc_final: 0.7512 (tmm) REVERT: E 110 ARG cc_start: 0.7482 (ttm110) cc_final: 0.6728 (mtp85) REVERT: E 112 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6695 (mp0) REVERT: E 127 TRP cc_start: 0.4997 (t60) cc_final: 0.4721 (t60) REVERT: E 324 MET cc_start: 0.8104 (ttm) cc_final: 0.7892 (ttm) REVERT: E 363 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7507 (mp0) REVERT: E 377 LYS cc_start: 0.7488 (mttp) cc_final: 0.6682 (mtmt) REVERT: F 1 MET cc_start: 0.3643 (tpt) cc_final: 0.3431 (tpt) REVERT: F 195 GLN cc_start: 0.6992 (mp10) cc_final: 0.6467 (mt0) REVERT: F 214 GLN cc_start: 0.6591 (tm-30) cc_final: 0.6217 (tt0) REVERT: F 256 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: F 267 MET cc_start: 0.8847 (mtt) cc_final: 0.8592 (mtt) REVERT: F 278 SER cc_start: 0.8571 (t) cc_final: 0.8289 (p) REVERT: F 355 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7233 (mt0) outliers start: 42 outliers final: 9 residues processed: 277 average time/residue: 1.4833 time to fit residues: 455.4981 Evaluate side-chains 242 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 263 GLN B 253 HIS B 307 ASN C 130 GLN D 16 GLN D 302 ASN ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 18480 Z= 0.602 Angle : 0.826 14.166 25041 Z= 0.418 Chirality : 0.052 0.205 2769 Planarity : 0.008 0.101 3195 Dihedral : 8.759 82.237 2547 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 4.26 % Allowed : 15.09 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.21 (0.17), residues: 2201 helix: 0.02 (0.18), residues: 767 sheet: -0.66 (0.22), residues: 487 loop : -1.49 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 158 HIS 0.015 0.002 HIS B 269 PHE 0.037 0.003 PHE A 296 TYR 0.018 0.003 TYR B 163 ARG 0.015 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 231 time to evaluate : 1.802 Fit side-chains REVERT: A 4 ASP cc_start: 0.8189 (t0) cc_final: 0.7966 (m-30) REVERT: A 18 ASP cc_start: 0.7849 (m-30) cc_final: 0.7636 (m-30) REVERT: A 25 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 59 TYR cc_start: 0.7982 (m-80) cc_final: 0.7482 (m-80) REVERT: A 63 LYS cc_start: 0.7886 (mttm) cc_final: 0.7384 (mtpt) REVERT: A 110 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6592 (ttm170) REVERT: A 120 MET cc_start: 0.7536 (mmm) cc_final: 0.7302 (mmm) REVERT: A 134 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6861 (mtp180) REVERT: A 231 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: A 256 GLU cc_start: 0.8744 (pt0) cc_final: 0.8285 (pt0) REVERT: A 308 ASP cc_start: 0.8042 (m-30) cc_final: 0.7794 (m-30) REVERT: A 334 ILE cc_start: 0.8358 (tt) cc_final: 0.7757 (pt) REVERT: B 18 ASP cc_start: 0.7839 (m-30) cc_final: 0.7540 (m-30) REVERT: B 84 GLU cc_start: 0.7887 (pt0) cc_final: 0.7534 (pt0) REVERT: B 110 ARG cc_start: 0.7453 (ttm110) cc_final: 0.6704 (ttt180) REVERT: B 129 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 133 LYS cc_start: 0.7440 (ttmm) cc_final: 0.6146 (mmtt) REVERT: B 236 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7087 (mt0) REVERT: B 324 MET cc_start: 0.7631 (mtm) cc_final: 0.6764 (mmm) REVERT: B 336 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7618 (tp40) REVERT: C 77 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6269 (mtp-110) REVERT: C 110 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.6720 (mtp85) REVERT: C 112 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6636 (mp0) REVERT: C 145 GLU cc_start: 0.6805 (pm20) cc_final: 0.6492 (pt0) REVERT: C 190 THR cc_start: 0.7552 (m) cc_final: 0.7227 (p) REVERT: C 244 CYS cc_start: 0.7419 (t) cc_final: 0.6687 (m) REVERT: C 282 ASP cc_start: 0.7989 (m-30) cc_final: 0.7754 (m-30) REVERT: C 377 LYS cc_start: 0.7815 (mtmm) cc_final: 0.6651 (tppt) REVERT: D 106 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5856 (tpp) REVERT: D 120 MET cc_start: 0.5620 (tpp) cc_final: 0.5256 (ttt) REVERT: D 267 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: D 271 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: D 355 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6995 (mp10) REVERT: E 77 ARG cc_start: 0.7355 (mtp180) cc_final: 0.5940 (mtm-85) REVERT: E 84 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: E 106 MET cc_start: 0.8311 (ttm) cc_final: 0.7643 (tmm) REVERT: E 110 ARG cc_start: 0.7469 (ttm110) cc_final: 0.6730 (mtp85) REVERT: E 112 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6707 (mp0) REVERT: E 377 LYS cc_start: 0.7645 (mttp) cc_final: 0.6691 (mtmt) REVERT: F 68 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6501 (mtp85) REVERT: F 106 MET cc_start: 0.6283 (tpp) cc_final: 0.5942 (tpp) REVERT: F 195 GLN cc_start: 0.7554 (mp10) cc_final: 0.6816 (mt0) REVERT: F 214 GLN cc_start: 0.6652 (tm-30) cc_final: 0.6281 (tt0) REVERT: F 256 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: F 262 ASN cc_start: 0.8010 (t0) cc_final: 0.7779 (t0) REVERT: F 267 MET cc_start: 0.8853 (mtt) cc_final: 0.8637 (mtt) REVERT: F 271 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6820 (mp10) REVERT: F 278 SER cc_start: 0.8739 (t) cc_final: 0.8469 (p) REVERT: F 355 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7286 (mt0) outliers start: 83 outliers final: 38 residues processed: 296 average time/residue: 1.4494 time to fit residues: 475.9116 Evaluate side-chains 264 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 10.0000 chunk 120 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 ASN C 130 GLN D 16 GLN D 192 ASN D 302 ASN D 375 ASN F 210 HIS F 302 ASN F 307 ASN F 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18480 Z= 0.189 Angle : 0.531 8.460 25041 Z= 0.283 Chirality : 0.041 0.148 2769 Planarity : 0.005 0.055 3195 Dihedral : 8.074 85.821 2547 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.34 % Allowed : 16.63 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2201 helix: 0.37 (0.18), residues: 787 sheet: -0.49 (0.22), residues: 499 loop : -1.30 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 199 HIS 0.011 0.001 HIS E 269 PHE 0.024 0.001 PHE A 296 TYR 0.014 0.001 TYR B 163 ARG 0.007 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 230 time to evaluate : 2.226 Fit side-chains REVERT: A 18 ASP cc_start: 0.7812 (m-30) cc_final: 0.7608 (m-30) REVERT: A 59 TYR cc_start: 0.8001 (m-80) cc_final: 0.7674 (m-80) REVERT: A 63 LYS cc_start: 0.7869 (mttm) cc_final: 0.7390 (mtpt) REVERT: A 110 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6586 (ttt180) REVERT: A 134 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.6575 (mtp180) REVERT: A 231 MET cc_start: 0.8372 (mtm) cc_final: 0.7697 (mtp) REVERT: A 267 MET cc_start: 0.9147 (mtp) cc_final: 0.8718 (mtm) REVERT: B 18 ASP cc_start: 0.7825 (m-30) cc_final: 0.7553 (m-30) REVERT: B 110 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6656 (ttt180) REVERT: B 120 MET cc_start: 0.8266 (mmm) cc_final: 0.8048 (mmm) REVERT: B 236 GLN cc_start: 0.7689 (tm-30) cc_final: 0.6827 (mt0) REVERT: B 324 MET cc_start: 0.7456 (mtm) cc_final: 0.6760 (mmp) REVERT: B 336 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7628 (tp40) REVERT: B 369 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: C 5 LYS cc_start: 0.8170 (tttp) cc_final: 0.7783 (tttm) REVERT: C 16 GLN cc_start: 0.8029 (tt0) cc_final: 0.7597 (tm-30) REVERT: C 77 ARG cc_start: 0.7143 (mtt-85) cc_final: 0.5959 (mtm-85) REVERT: C 110 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.6735 (mtp85) REVERT: C 112 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6617 (mp0) REVERT: C 145 GLU cc_start: 0.6830 (pm20) cc_final: 0.5954 (mm-30) REVERT: C 190 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7161 (p) REVERT: C 377 LYS cc_start: 0.7816 (mtmm) cc_final: 0.6798 (tptt) REVERT: D 106 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5782 (tpp) REVERT: D 120 MET cc_start: 0.5748 (tpp) cc_final: 0.5350 (mtt) REVERT: D 267 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8492 (tpp) REVERT: D 271 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6921 (mt0) REVERT: D 355 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6936 (mt0) REVERT: E 77 ARG cc_start: 0.7317 (mtp180) cc_final: 0.5971 (mtm-85) REVERT: E 84 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: E 106 MET cc_start: 0.8252 (ttm) cc_final: 0.7557 (tmm) REVERT: E 110 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6734 (mtp85) REVERT: E 112 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6706 (mp0) REVERT: E 127 TRP cc_start: 0.5062 (t60) cc_final: 0.4826 (t60) REVERT: E 324 MET cc_start: 0.8246 (ttm) cc_final: 0.7820 (ttm) REVERT: E 377 LYS cc_start: 0.7760 (mttp) cc_final: 0.6812 (mtmt) REVERT: F 195 GLN cc_start: 0.7204 (mp10) cc_final: 0.6557 (mt0) REVERT: F 214 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6161 (tt0) REVERT: F 256 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: F 262 ASN cc_start: 0.7749 (t0) cc_final: 0.7515 (t0) REVERT: F 267 MET cc_start: 0.8786 (mtt) cc_final: 0.8568 (mtt) REVERT: F 271 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: F 278 SER cc_start: 0.8632 (t) cc_final: 0.8362 (p) REVERT: F 355 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7238 (mt0) outliers start: 65 outliers final: 24 residues processed: 279 average time/residue: 1.4534 time to fit residues: 450.4253 Evaluate side-chains 258 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 16 GLN D 302 ASN D 375 ASN F 210 HIS F 302 ASN F 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18480 Z= 0.287 Angle : 0.594 8.782 25041 Z= 0.308 Chirality : 0.043 0.154 2769 Planarity : 0.005 0.058 3195 Dihedral : 8.191 88.260 2547 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.70 % Allowed : 17.04 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.84 (0.17), residues: 2201 helix: 0.37 (0.18), residues: 778 sheet: -0.48 (0.22), residues: 494 loop : -1.31 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 199 HIS 0.011 0.002 HIS E 269 PHE 0.029 0.002 PHE A 296 TYR 0.015 0.001 TYR A 159 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 2.017 Fit side-chains REVERT: A 18 ASP cc_start: 0.7802 (m-30) cc_final: 0.7584 (m-30) REVERT: A 25 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 59 TYR cc_start: 0.7997 (m-80) cc_final: 0.7651 (m-80) REVERT: A 63 LYS cc_start: 0.7876 (mttm) cc_final: 0.7390 (mtpt) REVERT: A 110 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6615 (ttt180) REVERT: A 134 ARG cc_start: 0.7130 (mmm-85) cc_final: 0.6710 (mtp180) REVERT: A 231 MET cc_start: 0.8407 (mtm) cc_final: 0.7824 (mtp) REVERT: A 334 ILE cc_start: 0.8304 (tt) cc_final: 0.7737 (pt) REVERT: B 18 ASP cc_start: 0.7857 (m-30) cc_final: 0.7593 (m-30) REVERT: B 110 ARG cc_start: 0.7397 (ttm110) cc_final: 0.6663 (ttt180) REVERT: B 133 LYS cc_start: 0.7358 (ttmm) cc_final: 0.5939 (mmtt) REVERT: B 236 GLN cc_start: 0.7754 (tm-30) cc_final: 0.6838 (mt0) REVERT: B 324 MET cc_start: 0.7426 (mtm) cc_final: 0.6606 (mmm) REVERT: B 336 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7662 (tp40) REVERT: C 5 LYS cc_start: 0.8177 (tttp) cc_final: 0.7793 (tttm) REVERT: C 16 GLN cc_start: 0.8006 (tt0) cc_final: 0.7562 (tm-30) REVERT: C 77 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.5862 (mtm-85) REVERT: C 110 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.6691 (mtp85) REVERT: C 112 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6562 (mp0) REVERT: C 145 GLU cc_start: 0.6839 (pm20) cc_final: 0.6044 (mm-30) REVERT: C 190 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7194 (p) REVERT: C 377 LYS cc_start: 0.7861 (mtmm) cc_final: 0.6649 (tppt) REVERT: D 85 MET cc_start: 0.7181 (mmm) cc_final: 0.6979 (tpt) REVERT: D 106 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5793 (tpp) REVERT: D 120 MET cc_start: 0.5752 (tpp) cc_final: 0.5293 (mtt) REVERT: D 262 ASN cc_start: 0.7872 (t0) cc_final: 0.7606 (t0) REVERT: D 267 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: D 271 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: D 355 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: E 77 ARG cc_start: 0.7302 (mtp180) cc_final: 0.5940 (mtm-85) REVERT: E 84 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: E 106 MET cc_start: 0.8254 (ttm) cc_final: 0.7561 (tmm) REVERT: E 110 ARG cc_start: 0.7478 (ttm110) cc_final: 0.6724 (mtp85) REVERT: E 112 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6548 (mp0) REVERT: E 127 TRP cc_start: 0.5077 (t60) cc_final: 0.4833 (t60) REVERT: E 324 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7879 (ttm) REVERT: E 377 LYS cc_start: 0.7748 (mttp) cc_final: 0.6818 (mtmt) REVERT: F 214 GLN cc_start: 0.6593 (tm-30) cc_final: 0.6184 (tt0) REVERT: F 256 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: F 262 ASN cc_start: 0.7846 (t0) cc_final: 0.7484 (t0) REVERT: F 267 MET cc_start: 0.8801 (mtt) cc_final: 0.8591 (mtt) REVERT: F 271 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6513 (mp10) REVERT: F 278 SER cc_start: 0.8646 (t) cc_final: 0.8375 (p) REVERT: F 355 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7230 (mt0) outliers start: 72 outliers final: 39 residues processed: 280 average time/residue: 1.4087 time to fit residues: 439.0939 Evaluate side-chains 272 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN C 307 ASN D 16 GLN D 302 ASN F 210 HIS F 302 ASN F 314 GLN F 344 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18480 Z= 0.265 Angle : 0.574 7.689 25041 Z= 0.299 Chirality : 0.043 0.152 2769 Planarity : 0.005 0.061 3195 Dihedral : 8.110 88.556 2547 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.85 % Allowed : 17.76 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.76 (0.17), residues: 2201 helix: 0.46 (0.19), residues: 770 sheet: -0.46 (0.22), residues: 493 loop : -1.27 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 199 HIS 0.012 0.001 HIS E 269 PHE 0.031 0.001 PHE A 296 TYR 0.015 0.001 TYR B 159 ARG 0.010 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 227 time to evaluate : 2.002 Fit side-chains REVERT: A 18 ASP cc_start: 0.7797 (m-30) cc_final: 0.7571 (m-30) REVERT: A 25 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 59 TYR cc_start: 0.8016 (m-80) cc_final: 0.7723 (m-80) REVERT: A 63 LYS cc_start: 0.7869 (mttm) cc_final: 0.7386 (mtpt) REVERT: A 110 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6615 (ttt180) REVERT: A 134 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6648 (mtp180) REVERT: A 231 MET cc_start: 0.8349 (mtm) cc_final: 0.7758 (mtp) REVERT: A 334 ILE cc_start: 0.8297 (tt) cc_final: 0.7725 (pt) REVERT: B 18 ASP cc_start: 0.7856 (m-30) cc_final: 0.7609 (m-30) REVERT: B 110 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6676 (ttt180) REVERT: B 133 LYS cc_start: 0.7414 (ttmm) cc_final: 0.5940 (mmtt) REVERT: B 236 GLN cc_start: 0.7753 (tm-30) cc_final: 0.6830 (mt0) REVERT: B 324 MET cc_start: 0.7354 (mtm) cc_final: 0.6577 (mmm) REVERT: B 336 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7653 (tp40) REVERT: C 5 LYS cc_start: 0.8187 (tttp) cc_final: 0.7812 (tttm) REVERT: C 16 GLN cc_start: 0.7995 (tt0) cc_final: 0.7651 (pt0) REVERT: C 77 ARG cc_start: 0.7072 (mtt-85) cc_final: 0.5911 (mtm-85) REVERT: C 110 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.6663 (mtp85) REVERT: C 112 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6635 (mp0) REVERT: C 145 GLU cc_start: 0.6822 (pm20) cc_final: 0.6125 (mm-30) REVERT: C 190 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7034 (p) REVERT: C 377 LYS cc_start: 0.7870 (mtmm) cc_final: 0.6644 (tppt) REVERT: D 85 MET cc_start: 0.7154 (mmm) cc_final: 0.6935 (tpt) REVERT: D 106 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5845 (tpp) REVERT: D 120 MET cc_start: 0.5830 (tpp) cc_final: 0.5258 (mtt) REVERT: D 262 ASN cc_start: 0.7860 (t0) cc_final: 0.7461 (t0) REVERT: D 267 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8589 (tpp) REVERT: D 271 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6854 (mt0) REVERT: D 355 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: E 77 ARG cc_start: 0.7260 (mtp180) cc_final: 0.6242 (mtp-110) REVERT: E 84 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7178 (mm-30) REVERT: E 106 MET cc_start: 0.8257 (ttm) cc_final: 0.7561 (tmm) REVERT: E 110 ARG cc_start: 0.7479 (ttm110) cc_final: 0.6716 (mtp85) REVERT: E 112 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6577 (mp0) REVERT: E 127 TRP cc_start: 0.5050 (t60) cc_final: 0.4826 (t60) REVERT: E 324 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7836 (ttm) REVERT: E 377 LYS cc_start: 0.7778 (mttp) cc_final: 0.6846 (mtmt) REVERT: F 68 ARG cc_start: 0.6981 (mtp85) cc_final: 0.5113 (mtm110) REVERT: F 214 GLN cc_start: 0.6593 (tm-30) cc_final: 0.6197 (tt0) REVERT: F 256 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: F 262 ASN cc_start: 0.7644 (t0) cc_final: 0.7426 (t0) REVERT: F 267 MET cc_start: 0.8824 (mtt) cc_final: 0.8601 (mtt) REVERT: F 271 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: F 278 SER cc_start: 0.8636 (t) cc_final: 0.8330 (p) REVERT: F 355 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7228 (mt0) outliers start: 75 outliers final: 37 residues processed: 284 average time/residue: 1.4170 time to fit residues: 447.8688 Evaluate side-chains 267 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 16 GLN D 302 ASN F 210 HIS F 302 ASN F 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18480 Z= 0.238 Angle : 0.563 8.572 25041 Z= 0.292 Chirality : 0.042 0.149 2769 Planarity : 0.005 0.055 3195 Dihedral : 7.978 85.517 2547 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.64 % Allowed : 18.33 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.17), residues: 2201 helix: 0.51 (0.19), residues: 770 sheet: -0.46 (0.22), residues: 494 loop : -1.24 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 199 HIS 0.012 0.001 HIS E 269 PHE 0.030 0.001 PHE B 296 TYR 0.015 0.001 TYR B 159 ARG 0.009 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 225 time to evaluate : 2.032 Fit side-chains REVERT: A 18 ASP cc_start: 0.7796 (m-30) cc_final: 0.7566 (m-30) REVERT: A 25 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7839 (tp) REVERT: A 59 TYR cc_start: 0.8015 (m-80) cc_final: 0.7712 (m-80) REVERT: A 63 LYS cc_start: 0.7866 (mttm) cc_final: 0.7383 (mtpt) REVERT: A 110 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6625 (ttt180) REVERT: A 134 ARG cc_start: 0.7058 (mmm-85) cc_final: 0.6641 (mtp180) REVERT: A 231 MET cc_start: 0.8387 (mtm) cc_final: 0.7700 (mtp) REVERT: A 334 ILE cc_start: 0.8255 (tt) cc_final: 0.7707 (pt) REVERT: B 18 ASP cc_start: 0.7849 (m-30) cc_final: 0.7606 (m-30) REVERT: B 110 ARG cc_start: 0.7405 (ttm110) cc_final: 0.6675 (ttt180) REVERT: B 133 LYS cc_start: 0.7327 (ttmm) cc_final: 0.5798 (mmtt) REVERT: B 236 GLN cc_start: 0.7754 (tm-30) cc_final: 0.6824 (mt0) REVERT: B 324 MET cc_start: 0.7332 (mtm) cc_final: 0.6579 (mmm) REVERT: B 336 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7647 (tp40) REVERT: C 5 LYS cc_start: 0.8204 (tttp) cc_final: 0.7832 (tttm) REVERT: C 16 GLN cc_start: 0.8011 (tt0) cc_final: 0.7679 (pt0) REVERT: C 77 ARG cc_start: 0.7067 (mtt-85) cc_final: 0.5906 (mtm-85) REVERT: C 110 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.6654 (mtp85) REVERT: C 112 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6567 (mp0) REVERT: C 145 GLU cc_start: 0.6804 (pm20) cc_final: 0.6557 (pt0) REVERT: C 190 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7002 (p) REVERT: C 336 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7006 (mm110) REVERT: C 377 LYS cc_start: 0.7878 (mtmm) cc_final: 0.6669 (tppt) REVERT: D 106 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5924 (tpp) REVERT: D 120 MET cc_start: 0.5884 (tpp) cc_final: 0.5201 (mtt) REVERT: D 262 ASN cc_start: 0.7669 (t0) cc_final: 0.7323 (t0) REVERT: D 267 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8630 (tpp) REVERT: D 271 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: D 355 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: E 77 ARG cc_start: 0.7268 (mtp180) cc_final: 0.6228 (mtp-110) REVERT: E 84 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: E 106 MET cc_start: 0.8255 (ttm) cc_final: 0.7569 (tmm) REVERT: E 110 ARG cc_start: 0.7477 (ttm110) cc_final: 0.6713 (mtp85) REVERT: E 112 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6583 (mp0) REVERT: E 127 TRP cc_start: 0.5027 (t60) cc_final: 0.4811 (t60) REVERT: E 324 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7882 (ttm) REVERT: E 377 LYS cc_start: 0.7783 (mttp) cc_final: 0.6864 (mtmt) REVERT: F 5 LYS cc_start: 0.8237 (pttp) cc_final: 0.7734 (ptpp) REVERT: F 68 ARG cc_start: 0.6959 (mtp85) cc_final: 0.5110 (mtm110) REVERT: F 214 GLN cc_start: 0.6634 (tm-30) cc_final: 0.6225 (tt0) REVERT: F 256 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: F 262 ASN cc_start: 0.7628 (t0) cc_final: 0.7334 (t0) REVERT: F 267 MET cc_start: 0.8826 (mtt) cc_final: 0.8614 (mtt) REVERT: F 271 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: F 278 SER cc_start: 0.8625 (t) cc_final: 0.8312 (p) REVERT: F 355 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7225 (mt0) outliers start: 71 outliers final: 40 residues processed: 282 average time/residue: 1.4388 time to fit residues: 458.3288 Evaluate side-chains 271 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 178 optimal weight: 0.0770 chunk 186 optimal weight: 0.9990 chunk 196 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 16 GLN D 302 ASN F 210 HIS F 302 ASN F 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18480 Z= 0.145 Angle : 0.486 7.190 25041 Z= 0.258 Chirality : 0.040 0.142 2769 Planarity : 0.005 0.053 3195 Dihedral : 7.621 81.143 2547 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.52 % Allowed : 19.66 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.48 (0.17), residues: 2201 helix: 0.70 (0.19), residues: 788 sheet: -0.35 (0.23), residues: 488 loop : -1.12 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 199 HIS 0.013 0.001 HIS E 269 PHE 0.020 0.001 PHE A 296 TYR 0.012 0.001 TYR A 159 ARG 0.009 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 2.077 Fit side-chains REVERT: A 18 ASP cc_start: 0.7798 (m-30) cc_final: 0.7584 (m-30) REVERT: A 59 TYR cc_start: 0.7993 (m-80) cc_final: 0.7713 (m-80) REVERT: A 63 LYS cc_start: 0.7819 (mttm) cc_final: 0.7360 (mtpt) REVERT: A 110 ARG cc_start: 0.7187 (ttm110) cc_final: 0.6588 (ttt180) REVERT: A 134 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6571 (ttp-170) REVERT: A 231 MET cc_start: 0.8276 (mtm) cc_final: 0.7711 (mtp) REVERT: A 282 ASP cc_start: 0.7885 (m-30) cc_final: 0.7558 (m-30) REVERT: B 18 ASP cc_start: 0.7817 (m-30) cc_final: 0.7616 (m-30) REVERT: B 110 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6647 (ttt180) REVERT: B 209 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6509 (tt0) REVERT: B 236 GLN cc_start: 0.7734 (tm-30) cc_final: 0.6791 (mt0) REVERT: B 324 MET cc_start: 0.7240 (mtm) cc_final: 0.6556 (mmp) REVERT: C 5 LYS cc_start: 0.8201 (tttp) cc_final: 0.7776 (tttm) REVERT: C 16 GLN cc_start: 0.7985 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 77 ARG cc_start: 0.7115 (mtt-85) cc_final: 0.5940 (mtm-85) REVERT: C 110 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.6642 (mtp85) REVERT: C 112 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6560 (mp0) REVERT: C 145 GLU cc_start: 0.6655 (pm20) cc_final: 0.6378 (pt0) REVERT: C 190 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 336 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6971 (mm110) REVERT: C 377 LYS cc_start: 0.7792 (mtmm) cc_final: 0.6807 (tptt) REVERT: D 74 LEU cc_start: 0.7384 (mp) cc_final: 0.7125 (mm) REVERT: D 106 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5941 (tpp) REVERT: D 262 ASN cc_start: 0.7588 (t0) cc_final: 0.7305 (t0) REVERT: D 267 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8667 (tpp) REVERT: D 271 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: E 77 ARG cc_start: 0.7179 (mtp180) cc_final: 0.5926 (mtm-85) REVERT: E 84 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: E 102 THR cc_start: 0.7855 (m) cc_final: 0.7554 (p) REVERT: E 106 MET cc_start: 0.8231 (ttm) cc_final: 0.7547 (tmm) REVERT: E 110 ARG cc_start: 0.7477 (ttm110) cc_final: 0.6704 (mtp85) REVERT: E 112 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6561 (mp0) REVERT: E 324 MET cc_start: 0.7979 (ttm) cc_final: 0.7759 (ttm) REVERT: E 377 LYS cc_start: 0.7766 (mttp) cc_final: 0.6835 (mtmt) REVERT: F 68 ARG cc_start: 0.7029 (mtp85) cc_final: 0.5248 (mtm110) REVERT: F 214 GLN cc_start: 0.6583 (tm-30) cc_final: 0.6079 (tt0) REVERT: F 256 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: F 262 ASN cc_start: 0.7534 (t0) cc_final: 0.7315 (t0) REVERT: F 278 SER cc_start: 0.8538 (t) cc_final: 0.8232 (p) outliers start: 49 outliers final: 23 residues processed: 271 average time/residue: 1.4226 time to fit residues: 428.9864 Evaluate side-chains 256 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 226 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 16 GLN D 302 ASN E 139 HIS F 210 HIS F 302 ASN F 307 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18480 Z= 0.426 Angle : 0.722 15.115 25041 Z= 0.363 Chirality : 0.047 0.159 2769 Planarity : 0.006 0.079 3195 Dihedral : 8.175 80.488 2547 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.77 % Allowed : 19.56 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.17), residues: 2201 helix: 0.31 (0.19), residues: 769 sheet: -0.54 (0.22), residues: 495 loop : -1.31 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 158 HIS 0.014 0.002 HIS C 269 PHE 0.040 0.002 PHE B 296 TYR 0.019 0.002 TYR B 159 ARG 0.009 0.001 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 223 time to evaluate : 2.057 Fit side-chains REVERT: A 18 ASP cc_start: 0.7836 (m-30) cc_final: 0.7624 (m-30) REVERT: A 25 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 59 TYR cc_start: 0.7936 (m-80) cc_final: 0.7607 (m-80) REVERT: A 63 LYS cc_start: 0.7886 (mttm) cc_final: 0.7395 (mtpt) REVERT: A 110 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6637 (ttt180) REVERT: A 134 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6687 (mtp180) REVERT: A 231 MET cc_start: 0.8442 (mtm) cc_final: 0.7870 (mtp) REVERT: A 334 ILE cc_start: 0.8380 (tt) cc_final: 0.7782 (pt) REVERT: B 18 ASP cc_start: 0.7862 (m-30) cc_final: 0.7592 (m-30) REVERT: B 110 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6686 (ttt180) REVERT: B 133 LYS cc_start: 0.7381 (ttmm) cc_final: 0.5870 (mmtt) REVERT: B 236 GLN cc_start: 0.7775 (tm-30) cc_final: 0.6920 (mt0) REVERT: B 324 MET cc_start: 0.7496 (mtm) cc_final: 0.6711 (mmm) REVERT: B 336 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7709 (tp40) REVERT: C 16 GLN cc_start: 0.7941 (tt0) cc_final: 0.7597 (pt0) REVERT: C 77 ARG cc_start: 0.7040 (mtt-85) cc_final: 0.6023 (mtm-85) REVERT: C 110 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.6622 (mtp85) REVERT: C 145 GLU cc_start: 0.6828 (pm20) cc_final: 0.6586 (pt0) REVERT: C 190 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7181 (p) REVERT: C 282 ASP cc_start: 0.8008 (m-30) cc_final: 0.7754 (m-30) REVERT: C 336 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7082 (mm110) REVERT: C 377 LYS cc_start: 0.7825 (mtmm) cc_final: 0.6651 (tppt) REVERT: D 106 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5989 (tpp) REVERT: D 120 MET cc_start: 0.5125 (mmm) cc_final: 0.4421 (mmt) REVERT: D 267 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8666 (tpp) REVERT: D 271 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: E 77 ARG cc_start: 0.7256 (mtp180) cc_final: 0.6201 (mtp-110) REVERT: E 84 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: E 102 THR cc_start: 0.7737 (m) cc_final: 0.7476 (p) REVERT: E 106 MET cc_start: 0.8284 (ttm) cc_final: 0.7594 (tmm) REVERT: E 110 ARG cc_start: 0.7448 (ttm110) cc_final: 0.6709 (mtp85) REVERT: E 112 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6557 (mp0) REVERT: E 127 TRP cc_start: 0.5048 (t60) cc_final: 0.4828 (t60) REVERT: E 377 LYS cc_start: 0.7755 (mttp) cc_final: 0.6833 (mtmt) REVERT: F 5 LYS cc_start: 0.8254 (pttp) cc_final: 0.7752 (ptpp) REVERT: F 120 MET cc_start: 0.5584 (tpp) cc_final: 0.5326 (mtt) REVERT: F 214 GLN cc_start: 0.6706 (tm-30) cc_final: 0.6272 (tt0) REVERT: F 256 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: F 262 ASN cc_start: 0.7704 (t0) cc_final: 0.7402 (t0) REVERT: F 278 SER cc_start: 0.8650 (t) cc_final: 0.8345 (p) REVERT: F 355 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7218 (mt0) outliers start: 54 outliers final: 27 residues processed: 265 average time/residue: 1.4361 time to fit residues: 423.0000 Evaluate side-chains 255 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 0.0020 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 16 GLN D 302 ASN F 210 HIS F 262 ASN F 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.208268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135692 restraints weight = 17209.957| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.88 r_work: 0.3225 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18480 Z= 0.139 Angle : 0.499 13.015 25041 Z= 0.263 Chirality : 0.040 0.149 2769 Planarity : 0.005 0.055 3195 Dihedral : 7.604 78.121 2547 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.10 % Allowed : 20.59 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.51 (0.17), residues: 2201 helix: 0.64 (0.19), residues: 787 sheet: -0.37 (0.23), residues: 489 loop : -1.10 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 199 HIS 0.013 0.001 HIS E 269 PHE 0.019 0.001 PHE A 296 TYR 0.013 0.001 TYR B 159 ARG 0.010 0.000 ARG F 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7344.06 seconds wall clock time: 131 minutes 56.00 seconds (7916.00 seconds total)