Starting phenix.real_space_refine on Thu Mar 21 01:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6d_31478/03_2024/7f6d_31478.pdb" } resolution = 3.85 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 18292 2.51 5 N 5240 2.21 5 O 5324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 155": "OE1" <-> "OE2" Residue "H TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 272": "OE1" <-> "OE2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "F GLU 549": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 528": "OE1" <-> "OE2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28930 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2528 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2528 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 14.79, per 1000 atoms: 0.51 Number of scatterers: 28930 At special positions: 0 Unit cell: (129.792, 126.75, 154.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 5324 8.00 N 5240 7.00 C 18292 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: 10.83 Conformation dependent library (CDL) restraints added in 5.1 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 22 sheets defined 36.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 209 through 219 removed outlier: 3.582A pdb=" N GLY H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.794A pdb=" N GLY H 294 " --> pdb=" O ALA H 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER H 298 " --> pdb=" O GLY H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 328 removed outlier: 3.546A pdb=" N GLN H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 344 removed outlier: 3.616A pdb=" N VAL H 334 " --> pdb=" O ASN H 330 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 343 " --> pdb=" O ARG H 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 163 removed outlier: 4.088A pdb=" N MET G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 219 removed outlier: 3.651A pdb=" N GLY G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 286 through 301 removed outlier: 3.781A pdb=" N GLY G 294 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER G 298 " --> pdb=" O GLY G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 328 removed outlier: 3.715A pdb=" N ALA G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 319 " --> pdb=" O ILE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 344 removed outlier: 3.580A pdb=" N VAL G 334 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 343 " --> pdb=" O ARG G 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.815A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.792A pdb=" N ALA B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.913A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.534A pdb=" N GLN B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 4.237A pdb=" N GLU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.079A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.590A pdb=" N PHE B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 335 removed outlier: 3.667A pdb=" N VAL B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.555A pdb=" N GLU B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 423 Proline residue: B 420 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.603A pdb=" N VAL B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.763A pdb=" N TYR B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.648A pdb=" N VAL B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.529A pdb=" N ARG B 556 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 removed outlier: 4.069A pdb=" N GLY B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.952A pdb=" N ALA A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.898A pdb=" N ILE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.568A pdb=" N TYR A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 218 through 222 removed outlier: 4.264A pdb=" N LEU A 221 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 229 through 243 removed outlier: 4.276A pdb=" N GLU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 316 through 335 Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 408 through 423 Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.836A pdb=" N VAL A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.990A pdb=" N VAL A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.666A pdb=" N GLY A 567 " --> pdb=" O ARG A 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.594A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.601A pdb=" N ALA C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.908A pdb=" N ILE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 removed outlier: 3.543A pdb=" N TYR C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.594A pdb=" N ALA C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 4.280A pdb=" N LEU C 221 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.565A pdb=" N GLU C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 316 through 335 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 530 through 536 removed outlier: 3.789A pdb=" N VAL C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 556 removed outlier: 4.253A pdb=" N GLU C 551 " --> pdb=" O ALA C 548 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Proline residue: C 553 - end of helix Processing helix chain 'C' and resid 562 through 567 removed outlier: 4.645A pdb=" N GLY C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 175 through 190 removed outlier: 4.200A pdb=" N GLY E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.975A pdb=" N LEU E 221 " --> pdb=" O GLY E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.893A pdb=" N GLU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 267 through 275 Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 316 through 335 removed outlier: 3.612A pdb=" N GLN E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 387 removed outlier: 3.938A pdb=" N ARG E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.806A pdb=" N VAL E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Proline residue: E 420 - end of helix Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 488 through 493 removed outlier: 4.207A pdb=" N TYR E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 511 removed outlier: 3.584A pdb=" N VAL E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 537 removed outlier: 3.598A pdb=" N VAL E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 537 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 562 through 567 removed outlier: 4.500A pdb=" N GLY E 567 " --> pdb=" O ARG E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'F' and resid 175 through 190 removed outlier: 4.075A pdb=" N GLY F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 218 through 222 removed outlier: 4.096A pdb=" N LEU F 221 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 243 removed outlier: 3.552A pdb=" N GLU F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 294 through 302 removed outlier: 3.856A pdb=" N ARG F 302 " --> pdb=" O PHE F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 3.560A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 386 Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.680A pdb=" N ARG F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) Proline residue: F 420 - end of helix Processing helix chain 'F' and resid 454 through 476 removed outlier: 3.651A pdb=" N GLY F 463 " --> pdb=" O MET F 459 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 476 " --> pdb=" O TYR F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 493 removed outlier: 4.220A pdb=" N TYR F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 511 removed outlier: 3.710A pdb=" N VAL F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 536 removed outlier: 3.889A pdb=" N VAL F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 556 removed outlier: 3.855A pdb=" N GLU F 551 " --> pdb=" O ALA F 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 552 " --> pdb=" O GLU F 549 " (cutoff:3.500A) Proline residue: F 553 - end of helix Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 562 through 567 removed outlier: 4.561A pdb=" N GLY F 567 " --> pdb=" O ARG F 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.805A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.814A pdb=" N ALA D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.905A pdb=" N ALA D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.526A pdb=" N GLN D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.229A pdb=" N GLU D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.088A pdb=" N THR D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.623A pdb=" N PHE D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.615A pdb=" N VAL D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.560A pdb=" N GLU D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 423 Proline residue: D 420 - end of helix Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.590A pdb=" N VAL D 476 " --> pdb=" O TYR D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.672A pdb=" N TYR D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 512 Processing helix chain 'D' and resid 530 through 537 removed outlier: 3.639A pdb=" N VAL D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 556 removed outlier: 3.526A pdb=" N ARG D 556 " --> pdb=" O PRO D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 removed outlier: 4.065A pdb=" N GLY D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.581A pdb=" N THR H 12 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 95 through 103 removed outlier: 7.002A pdb=" N ALA H 83 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL H 99 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL H 81 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA H 101 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR H 79 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP H 184 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLY H 54 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY H 198 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG H 270 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP H 251 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN H 247 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA4, first strand: chain 'G' and resid 95 through 103 removed outlier: 6.980A pdb=" N ALA G 83 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL G 99 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL G 81 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA G 101 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR G 79 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU G 48 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU G 182 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 50 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP G 184 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL G 52 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP G 251 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN G 247 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 5.329A pdb=" N TYR B 93 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 92 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 68 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA B 94 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL B 66 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 96 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 64 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 60 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 102 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG B 58 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 48 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS B 115 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 116 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B 16 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.150A pdb=" N LEU B 151 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 141 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 289 through 290 removed outlier: 8.046A pdb=" N THR B 289 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU B 264 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 263 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 449 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 265 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 211 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 448 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 213 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 214 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 482 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 520 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 484 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA B 522 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU B 486 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 574 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 16 through 17 removed outlier: 4.742A pdb=" N TYR A 93 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER A 92 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 68 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA A 94 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 66 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG A 96 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 64 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR A 60 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL A 102 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 58 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 48 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS A 115 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 116 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A 16 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 138 through 142 removed outlier: 6.942A pdb=" N LEU A 149 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 264 through 265 removed outlier: 6.564A pdb=" N LEU A 265 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A 448 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 213 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 210 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL A 485 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 212 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 16 through 17 removed outlier: 4.758A pdb=" N TYR C 93 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN C 65 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 98 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL C 63 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR C 100 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY C 61 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 102 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE C 59 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 48 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS C 115 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 116 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 16 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.978A pdb=" N LEU C 149 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 264 through 265 removed outlier: 8.715A pdb=" N VAL C 448 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 213 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG C 210 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL C 485 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 212 " --> pdb=" O VAL C 485 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.228A pdb=" N SER E 90 " --> pdb=" O HIS E 70 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS E 70 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER E 92 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS E 68 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA E 94 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL E 66 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG E 96 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 64 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR E 60 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL E 102 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG E 58 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 43 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.535A pdb=" N LEU E 149 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 289 through 290 removed outlier: 6.387A pdb=" N LEU E 264 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 449 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA E 211 " --> pdb=" O THR E 446 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 448 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE E 213 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG E 210 " --> pdb=" O PHE E 483 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 485 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 212 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE E 164 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLN E 523 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE E 166 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 31 through 32 removed outlier: 5.917A pdb=" N SER F 90 " --> pdb=" O HIS F 70 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS F 70 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER F 92 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS F 68 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA F 94 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL F 66 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG F 96 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 64 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR F 60 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL F 102 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG F 58 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP F 43 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 137 through 142 removed outlier: 6.575A pdb=" N LEU F 149 " --> pdb=" O GLY F 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 289 through 290 removed outlier: 8.265A pdb=" N THR F 289 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 264 " --> pdb=" O THR F 289 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA F 211 " --> pdb=" O THR F 446 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 448 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 213 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG F 210 " --> pdb=" O PHE F 483 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL F 485 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 212 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 164 " --> pdb=" O GLY F 521 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS F 163 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL F 541 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN F 165 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY F 543 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER F 167 " --> pdb=" O GLY F 543 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN F 578 " --> pdb=" O ASN F 583 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN F 583 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 16 through 18 removed outlier: 5.287A pdb=" N TYR D 93 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER D 92 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS D 68 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA D 94 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL D 66 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG D 96 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP D 64 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR D 60 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL D 102 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG D 58 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 48 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HIS D 115 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 116 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 16 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.171A pdb=" N LEU D 151 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY D 141 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 289 through 290 removed outlier: 8.042A pdb=" N THR D 289 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU D 264 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN D 263 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP D 449 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 265 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 211 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 448 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE D 213 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 214 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 482 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 520 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 484 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA D 522 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU D 486 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 574 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2916 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: 9.33 Time building geometry restraints manager: 11.62 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: 9904 1.34 - 1.46: 3314 1.46 - 1.57: 16132 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 29486 Sorted by residual: bond pdb=" C ASP G 257 " pdb=" N ALA G 258 " ideal model delta sigma weight residual 1.331 1.258 0.073 2.07e-02 2.33e+03 1.24e+01 bond pdb=" C PRO G 259 " pdb=" N PHE G 260 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.31e-02 5.83e+03 4.08e+00 bond pdb=" C LEU E 304 " pdb=" N PRO E 305 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.39e+00 bond pdb=" C LEU B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 bond pdb=" CB PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.42e+00 ... (remaining 29481 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.13: 956 106.13 - 113.09: 15638 113.09 - 120.06: 10002 120.06 - 127.03: 13069 127.03 - 133.99: 315 Bond angle restraints: 39980 Sorted by residual: angle pdb=" N PRO G 9 " pdb=" CA PRO G 9 " pdb=" CB PRO G 9 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N LEU G 128 " pdb=" CA LEU G 128 " pdb=" C LEU G 128 " ideal model delta sigma weight residual 108.34 113.33 -4.99 1.31e+00 5.83e-01 1.45e+01 angle pdb=" C PRO A 579 " pdb=" N ASP A 580 " pdb=" CA ASP A 580 " ideal model delta sigma weight residual 125.66 132.58 -6.92 1.85e+00 2.92e-01 1.40e+01 angle pdb=" N ASN G 122 " pdb=" CA ASN G 122 " pdb=" C ASN G 122 " ideal model delta sigma weight residual 109.81 117.60 -7.79 2.21e+00 2.05e-01 1.24e+01 ... (remaining 39975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16158 17.95 - 35.91: 1452 35.91 - 53.86: 202 53.86 - 71.81: 28 71.81 - 89.77: 16 Dihedral angle restraints: 17856 sinusoidal: 7108 harmonic: 10748 Sorted by residual: dihedral pdb=" CA LYS H 303 " pdb=" C LYS H 303 " pdb=" N LEU H 304 " pdb=" CA LEU H 304 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU F 304 " pdb=" C LEU F 304 " pdb=" N PRO F 305 " pdb=" CA PRO F 305 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ASN G 122 " pdb=" C ASN G 122 " pdb=" N PRO G 123 " pdb=" CA PRO G 123 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 17853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3651 0.051 - 0.102: 678 0.102 - 0.153: 171 0.153 - 0.203: 3 0.203 - 0.254: 3 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CA ASN G 122 " pdb=" N ASN G 122 " pdb=" C ASN G 122 " pdb=" CB ASN G 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO G 9 " pdb=" N PRO G 9 " pdb=" C PRO G 9 " pdb=" CB PRO G 9 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4503 not shown) Planarity restraints: 5318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 103 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO F 104 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 104 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 104 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 122 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO G 123 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 103 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO E 104 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 104 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 104 " -0.020 5.00e-02 4.00e+02 ... (remaining 5315 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3344 2.75 - 3.29: 29137 3.29 - 3.83: 44715 3.83 - 4.36: 50515 4.36 - 4.90: 87821 Nonbonded interactions: 215532 Sorted by model distance: nonbonded pdb=" O VAL B 39 " pdb=" OH TYR B 93 " model vdw 2.214 2.440 nonbonded pdb=" O GLN C 415 " pdb=" OG SER C 419 " model vdw 2.214 2.440 nonbonded pdb=" O SER A 185 " pdb=" OG SER A 189 " model vdw 2.216 2.440 nonbonded pdb=" O LEU H 118 " pdb=" NH2 ARG H 337 " model vdw 2.227 2.520 nonbonded pdb=" OD2 ASP H 53 " pdb=" OG1 THR H 317 " model vdw 2.229 2.440 ... (remaining 215527 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.030 Extract box with map and model: 5.730 Check model and map are aligned: 0.350 Set scattering table: 0.300 Process input model: 72.300 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.002 0.073 29486 Z= 0.152 Angle : 0.588 8.433 39980 Z= 0.291 Chirality : 0.042 0.254 4506 Planarity : 0.003 0.044 5318 Dihedral : 13.431 89.768 10952 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3734 helix: 0.33 (0.16), residues: 1078 sheet: 0.37 (0.21), residues: 680 loop : -1.64 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 34 HIS 0.004 0.000 HIS H 305 PHE 0.016 0.001 PHE E 291 TYR 0.018 0.001 TYR D 306 ARG 0.009 0.000 ARG F 441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7564 (ptt90) REVERT: B 503 ASP cc_start: 0.7375 (p0) cc_final: 0.7136 (p0) REVERT: C 409 ARG cc_start: 0.7678 (mtt90) cc_final: 0.7261 (mtm-85) REVERT: E 17 MET cc_start: 0.8034 (mpp) cc_final: 0.7770 (mpp) REVERT: D 101 ARG cc_start: 0.7774 (ptt90) cc_final: 0.7559 (ptt90) REVERT: D 286 GLU cc_start: 0.7687 (tt0) cc_final: 0.7475 (tt0) REVERT: D 303 MET cc_start: 0.6725 (mmp) cc_final: 0.5448 (mmt) REVERT: D 306 TYR cc_start: 0.8652 (m-80) cc_final: 0.7717 (m-10) REVERT: D 503 ASP cc_start: 0.7427 (p0) cc_final: 0.7187 (p0) outliers start: 1 outliers final: 1 residues processed: 437 average time/residue: 0.4282 time to fit residues: 289.4389 Evaluate side-chains 344 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 153 optimal weight: 0.0770 chunk 296 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 220 optimal weight: 0.3980 chunk 343 optimal weight: 4.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS F 118 HIS ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29486 Z= 0.235 Angle : 0.636 12.028 39980 Z= 0.315 Chirality : 0.044 0.223 4506 Planarity : 0.004 0.041 5318 Dihedral : 4.201 54.188 4176 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 1.51 % Allowed : 9.40 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3734 helix: 0.76 (0.16), residues: 1062 sheet: -0.08 (0.19), residues: 762 loop : -1.74 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 34 HIS 0.014 0.001 HIS F 451 PHE 0.018 0.002 PHE B 407 TYR 0.019 0.002 TYR B 472 ARG 0.005 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 371 time to evaluate : 3.784 Fit side-chains revert: symmetry clash REVERT: B 563 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7604 (ttm110) REVERT: A 231 MET cc_start: 0.8583 (ppp) cc_final: 0.8295 (ppp) REVERT: A 536 ASN cc_start: 0.8095 (p0) cc_final: 0.7877 (p0) REVERT: C 411 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5869 (tp) REVERT: C 536 ASN cc_start: 0.8077 (p0) cc_final: 0.7846 (p0) REVERT: E 17 MET cc_start: 0.8105 (mpp) cc_final: 0.7822 (mpp) REVERT: D 303 MET cc_start: 0.6917 (mmp) cc_final: 0.5801 (mmt) REVERT: D 306 TYR cc_start: 0.8744 (m-10) cc_final: 0.7610 (m-10) REVERT: D 563 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7576 (ttm110) outliers start: 45 outliers final: 31 residues processed: 399 average time/residue: 0.4383 time to fit residues: 268.1549 Evaluate side-chains 371 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 339 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 343 optimal weight: 0.7980 chunk 371 optimal weight: 0.7980 chunk 306 optimal weight: 30.0000 chunk 341 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 275 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 HIS ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS F 118 HIS ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29486 Z= 0.240 Angle : 0.609 11.280 39980 Z= 0.298 Chirality : 0.043 0.237 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.134 24.157 4174 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.87 % Favored : 92.07 % Rotamer: Outliers : 1.84 % Allowed : 13.49 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3734 helix: 0.56 (0.15), residues: 1172 sheet: -0.20 (0.19), residues: 750 loop : -1.94 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 34 HIS 0.014 0.001 HIS F 451 PHE 0.016 0.001 PHE E 29 TYR 0.017 0.001 TYR G 130 ARG 0.014 0.000 ARG E 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 357 time to evaluate : 3.625 Fit side-chains revert: symmetry clash REVERT: B 563 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7685 (ttm110) REVERT: A 536 ASN cc_start: 0.8129 (p0) cc_final: 0.7904 (p0) REVERT: E 17 MET cc_start: 0.8119 (mpp) cc_final: 0.7777 (mpp) REVERT: D 303 MET cc_start: 0.7011 (mmp) cc_final: 0.5946 (mmt) REVERT: D 306 TYR cc_start: 0.8832 (m-10) cc_final: 0.7596 (m-10) REVERT: D 459 MET cc_start: 0.7573 (tpp) cc_final: 0.7043 (tpt) REVERT: D 563 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7679 (ttm110) outliers start: 55 outliers final: 45 residues processed: 397 average time/residue: 0.4271 time to fit residues: 262.1907 Evaluate side-chains 380 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 335 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 345 optimal weight: 8.9990 chunk 365 optimal weight: 0.0770 chunk 180 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29486 Z= 0.192 Angle : 0.588 11.296 39980 Z= 0.285 Chirality : 0.043 0.241 4506 Planarity : 0.003 0.038 5318 Dihedral : 4.058 23.700 4174 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 2.14 % Allowed : 15.63 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3734 helix: 0.70 (0.15), residues: 1184 sheet: -0.01 (0.20), residues: 696 loop : -1.93 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 34 HIS 0.014 0.001 HIS F 451 PHE 0.016 0.001 PHE F 308 TYR 0.018 0.001 TYR B 472 ARG 0.005 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 355 time to evaluate : 3.396 Fit side-chains revert: symmetry clash REVERT: G 304 LEU cc_start: 0.8836 (pp) cc_final: 0.8612 (pp) REVERT: B 459 MET cc_start: 0.7412 (tpp) cc_final: 0.7014 (tpt) REVERT: B 563 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7688 (ttm110) REVERT: C 488 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: E 17 MET cc_start: 0.8091 (mpp) cc_final: 0.7766 (mpp) REVERT: D 303 MET cc_start: 0.6851 (mmp) cc_final: 0.5967 (mmt) REVERT: D 306 TYR cc_start: 0.8806 (m-10) cc_final: 0.7559 (m-10) REVERT: D 459 MET cc_start: 0.7462 (tpp) cc_final: 0.7036 (tpt) REVERT: D 563 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7677 (ttm110) outliers start: 64 outliers final: 50 residues processed: 402 average time/residue: 0.4299 time to fit residues: 266.4280 Evaluate side-chains 385 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 334 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 272 optimal weight: 0.2980 chunk 150 optimal weight: 30.0000 chunk 311 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 chunk 327 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS C 415 GLN ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 29486 Z= 0.431 Angle : 0.714 11.315 39980 Z= 0.354 Chirality : 0.047 0.251 4506 Planarity : 0.005 0.044 5318 Dihedral : 4.652 26.068 4174 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.80 % Favored : 90.12 % Rotamer: Outliers : 3.05 % Allowed : 17.37 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3734 helix: 0.36 (0.15), residues: 1180 sheet: -0.45 (0.19), residues: 696 loop : -2.15 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 34 HIS 0.011 0.002 HIS D 70 PHE 0.025 0.002 PHE E 29 TYR 0.021 0.002 TYR D 589 ARG 0.006 0.001 ARG E 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 334 time to evaluate : 3.335 Fit side-chains revert: symmetry clash REVERT: H 206 ASP cc_start: 0.7180 (p0) cc_final: 0.6851 (p0) REVERT: G 304 LEU cc_start: 0.8902 (pp) cc_final: 0.8629 (pp) REVERT: B 459 MET cc_start: 0.7661 (tpp) cc_final: 0.7180 (tpt) REVERT: B 563 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7705 (ttm110) REVERT: A 409 ARG cc_start: 0.7454 (mtt90) cc_final: 0.7045 (mtm-85) REVERT: C 70 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7923 (t-90) REVERT: C 249 TYR cc_start: 0.8453 (m-80) cc_final: 0.8210 (m-80) REVERT: C 409 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7411 (mtm-85) REVERT: C 488 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: E 240 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.8099 (mtm110) REVERT: D 459 MET cc_start: 0.7739 (tpp) cc_final: 0.7277 (tpt) REVERT: D 563 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7701 (ttm110) outliers start: 91 outliers final: 76 residues processed: 406 average time/residue: 0.4246 time to fit residues: 266.7356 Evaluate side-chains 388 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 310 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 365 optimal weight: 0.9990 chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29486 Z= 0.259 Angle : 0.633 11.828 39980 Z= 0.309 Chirality : 0.044 0.257 4506 Planarity : 0.004 0.043 5318 Dihedral : 4.471 28.042 4174 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.54 % Favored : 91.40 % Rotamer: Outliers : 3.08 % Allowed : 18.44 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3734 helix: 0.55 (0.15), residues: 1184 sheet: -0.43 (0.19), residues: 696 loop : -2.09 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.012 0.001 HIS C 70 PHE 0.018 0.001 PHE E 29 TYR 0.019 0.001 TYR B 472 ARG 0.006 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 344 time to evaluate : 4.256 Fit side-chains revert: symmetry clash REVERT: H 206 ASP cc_start: 0.7068 (p0) cc_final: 0.6750 (p0) REVERT: G 304 LEU cc_start: 0.8883 (pp) cc_final: 0.8611 (pp) REVERT: B 459 MET cc_start: 0.7509 (tpp) cc_final: 0.7072 (tpt) REVERT: B 563 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7750 (ttm110) REVERT: A 249 TYR cc_start: 0.8345 (m-80) cc_final: 0.8001 (m-80) REVERT: A 409 ARG cc_start: 0.7445 (mtt90) cc_final: 0.6949 (mtm-85) REVERT: C 132 LYS cc_start: 0.7815 (mptt) cc_final: 0.7595 (mptt) REVERT: C 249 TYR cc_start: 0.8475 (m-80) cc_final: 0.8187 (m-80) REVERT: C 488 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: E 240 ARG cc_start: 0.8420 (ptp-110) cc_final: 0.8065 (mtm110) REVERT: D 459 MET cc_start: 0.7589 (tpp) cc_final: 0.7163 (tpt) REVERT: D 563 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7715 (ttm110) outliers start: 92 outliers final: 70 residues processed: 414 average time/residue: 0.4499 time to fit residues: 289.5820 Evaluate side-chains 394 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 323 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 ASN Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain F residue 588 ASN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29486 Z= 0.234 Angle : 0.621 12.046 39980 Z= 0.302 Chirality : 0.044 0.289 4506 Planarity : 0.004 0.042 5318 Dihedral : 4.363 29.127 4174 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.65 % Favored : 91.30 % Rotamer: Outliers : 3.01 % Allowed : 19.21 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3734 helix: 0.71 (0.15), residues: 1178 sheet: -0.43 (0.19), residues: 696 loop : -2.04 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 34 HIS 0.008 0.001 HIS F 451 PHE 0.016 0.001 PHE E 29 TYR 0.022 0.001 TYR B 472 ARG 0.006 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 344 time to evaluate : 3.774 Fit side-chains revert: symmetry clash REVERT: H 206 ASP cc_start: 0.7055 (p0) cc_final: 0.6732 (p0) REVERT: G 304 LEU cc_start: 0.8876 (pp) cc_final: 0.8580 (pp) REVERT: B 459 MET cc_start: 0.7465 (tpp) cc_final: 0.7026 (tpt) REVERT: A 249 TYR cc_start: 0.8343 (m-80) cc_final: 0.8002 (m-80) REVERT: A 409 ARG cc_start: 0.7316 (mtt90) cc_final: 0.7043 (mtm-85) REVERT: C 249 TYR cc_start: 0.8482 (m-80) cc_final: 0.8176 (m-80) REVERT: C 488 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: E 17 MET cc_start: 0.8291 (mpp) cc_final: 0.7946 (mpp) REVERT: E 240 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.8058 (mtm110) REVERT: F 222 LEU cc_start: 0.8250 (tp) cc_final: 0.7667 (mt) REVERT: D 459 MET cc_start: 0.7494 (tpp) cc_final: 0.7075 (tpt) outliers start: 90 outliers final: 78 residues processed: 415 average time/residue: 0.4244 time to fit residues: 273.1750 Evaluate side-chains 398 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 319 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 ASN Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain F residue 588 ASN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 0.0050 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 248 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 286 optimal weight: 4.9990 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 578 GLN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29486 Z= 0.166 Angle : 0.608 12.133 39980 Z= 0.293 Chirality : 0.043 0.221 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.167 28.313 4174 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 2.71 % Allowed : 19.98 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3734 helix: 0.90 (0.16), residues: 1178 sheet: -0.37 (0.20), residues: 702 loop : -1.94 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 34 HIS 0.018 0.001 HIS F 70 PHE 0.015 0.001 PHE H 22 TYR 0.026 0.001 TYR B 472 ARG 0.007 0.000 ARG D 563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 350 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 304 LEU cc_start: 0.8868 (pp) cc_final: 0.8575 (pp) REVERT: B 459 MET cc_start: 0.7308 (tpp) cc_final: 0.6919 (tpt) REVERT: A 409 ARG cc_start: 0.7269 (mtt90) cc_final: 0.6938 (mtm-85) REVERT: C 70 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7677 (t-90) REVERT: C 249 TYR cc_start: 0.8464 (m-80) cc_final: 0.8175 (m-80) REVERT: C 409 ARG cc_start: 0.7671 (mtt90) cc_final: 0.7235 (mtm-85) REVERT: C 488 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: E 17 MET cc_start: 0.8223 (mpp) cc_final: 0.7847 (mpp) REVERT: F 222 LEU cc_start: 0.8135 (tp) cc_final: 0.7601 (mt) REVERT: D 459 MET cc_start: 0.7368 (tpp) cc_final: 0.6955 (tpt) outliers start: 81 outliers final: 71 residues processed: 411 average time/residue: 0.4135 time to fit residues: 265.7320 Evaluate side-chains 395 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 322 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 306 optimal weight: 30.0000 chunk 321 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29486 Z= 0.189 Angle : 0.613 12.059 39980 Z= 0.294 Chirality : 0.043 0.195 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.116 28.070 4174 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 2.78 % Allowed : 20.15 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3734 helix: 0.91 (0.16), residues: 1184 sheet: -0.34 (0.20), residues: 702 loop : -1.94 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 34 HIS 0.009 0.001 HIS C 70 PHE 0.018 0.001 PHE E 75 TYR 0.026 0.001 TYR B 472 ARG 0.007 0.000 ARG F 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 344 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 206 ASP cc_start: 0.6916 (p0) cc_final: 0.6601 (p0) REVERT: G 304 LEU cc_start: 0.8847 (pp) cc_final: 0.8571 (pp) REVERT: B 459 MET cc_start: 0.7321 (tpp) cc_final: 0.6922 (tpt) REVERT: A 409 ARG cc_start: 0.7268 (mtt90) cc_final: 0.6965 (mtm-85) REVERT: C 249 TYR cc_start: 0.8509 (m-80) cc_final: 0.8185 (m-80) REVERT: C 488 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: E 17 MET cc_start: 0.8223 (mpp) cc_final: 0.7856 (mpp) REVERT: F 222 LEU cc_start: 0.8155 (tp) cc_final: 0.7603 (mt) REVERT: D 459 MET cc_start: 0.7353 (tpp) cc_final: 0.6936 (tpt) outliers start: 83 outliers final: 74 residues processed: 406 average time/residue: 0.4211 time to fit residues: 266.9817 Evaluate side-chains 398 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 323 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 359 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 376 optimal weight: 0.2980 chunk 346 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29486 Z= 0.238 Angle : 0.634 11.787 39980 Z= 0.306 Chirality : 0.044 0.196 4506 Planarity : 0.004 0.041 5318 Dihedral : 4.182 27.807 4174 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 2.78 % Allowed : 20.28 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3734 helix: 0.86 (0.16), residues: 1184 sheet: -0.44 (0.19), residues: 702 loop : -1.96 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 34 HIS 0.007 0.001 HIS F 451 PHE 0.019 0.001 PHE A 308 TYR 0.027 0.001 TYR B 472 ARG 0.008 0.000 ARG A 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 332 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 206 ASP cc_start: 0.7016 (p0) cc_final: 0.6692 (p0) REVERT: G 304 LEU cc_start: 0.8867 (pp) cc_final: 0.8589 (pp) REVERT: B 459 MET cc_start: 0.7386 (tpp) cc_final: 0.6960 (tpt) REVERT: A 249 TYR cc_start: 0.8401 (m-80) cc_final: 0.8072 (m-80) REVERT: A 409 ARG cc_start: 0.7293 (mtt90) cc_final: 0.6983 (mtm-85) REVERT: C 249 TYR cc_start: 0.8530 (m-80) cc_final: 0.8219 (m-80) REVERT: C 409 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7418 (mtm-85) REVERT: C 410 ARG cc_start: 0.6866 (mpp-170) cc_final: 0.6636 (mtm110) REVERT: C 488 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: E 17 MET cc_start: 0.8297 (mpp) cc_final: 0.7953 (mpp) REVERT: E 222 LEU cc_start: 0.8225 (tp) cc_final: 0.7778 (mt) REVERT: E 240 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8038 (mtm110) REVERT: D 303 MET cc_start: 0.6841 (mmp) cc_final: 0.6312 (mmp) REVERT: D 459 MET cc_start: 0.7409 (tpp) cc_final: 0.6970 (tpt) outliers start: 83 outliers final: 75 residues processed: 397 average time/residue: 0.4248 time to fit residues: 264.1494 Evaluate side-chains 389 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 588 ASN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 276 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133171 restraints weight = 50550.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133307 restraints weight = 43692.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134631 restraints weight = 44365.338| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29486 Z= 0.228 Angle : 0.634 11.771 39980 Z= 0.305 Chirality : 0.044 0.218 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.195 28.002 4174 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.51 % Rotamer: Outliers : 2.68 % Allowed : 20.68 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3734 helix: 0.86 (0.16), residues: 1184 sheet: -0.45 (0.19), residues: 702 loop : -1.97 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 34 HIS 0.007 0.001 HIS F 451 PHE 0.017 0.001 PHE B 29 TYR 0.028 0.001 TYR B 472 ARG 0.010 0.000 ARG F 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5455.97 seconds wall clock time: 99 minutes 12.22 seconds (5952.22 seconds total)