Starting phenix.real_space_refine (version: dev) on Tue Feb 28 03:18:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmq_25999/02_2023/7tmq_25999_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.147 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 Process input model Symmetric amino acids flipped Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 405": "OD1" <-> "OD2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31642 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4241 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 560} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 28, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3424 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 20, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4043 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 519 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 31, 'PHE:plan': 3, 'GLU:plan': 33, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 334 Chain: "D" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3320 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 25, 'ASN:plan1': 8, 'ARG:plan': 1, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 207 Chain: "E" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4117 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 553} Chain breaks: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 24, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 245 Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3300 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 26, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1063 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 16, 'ASN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 299 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1360 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "J" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 581 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "K" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1322 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 200 Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 486 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1286 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 566 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 284 Chain: "N" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 561 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 196 Chain: "P" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2211 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 1399 Unresolved non-hydrogen angles: 1785 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.84, per 1000 atoms: 0.56 Number of scatterers: 31642 At special positions: 0 Unit cell: (147.29, 136.99, 201.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 2 15.00 Mg 1 11.99 O 5561 8.00 N 5709 7.00 C 20279 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: 13.89 Conformation dependent library (CDL) restraints added in 5.9 seconds 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 37 sheets defined 48.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.611A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.854A pdb=" N GLU A 330 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 443 through 449 removed outlier: 4.559A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 4.033A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 4.098A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 567 through 582 removed outlier: 5.575A pdb=" N ASP A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 613 removed outlier: 3.657A pdb=" N ARG A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 19 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 250 through 270 removed outlier: 4.010A pdb=" N THR B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Proline residue: B 256 - end of helix removed outlier: 3.634A pdb=" N ALA B 267 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 268 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 269 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.485A pdb=" N ARG B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 396 through 420 Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 478 through 484 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 262 through 271 Processing helix chain 'C' and resid 287 through 299 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 326 through 345 removed outlier: 4.806A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 384 through 393 Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 464 through 473 removed outlier: 4.569A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 501 Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 540 through 563 Processing helix chain 'C' and resid 567 through 586 removed outlier: 5.490A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 612 removed outlier: 4.180A pdb=" N GLY C 598 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 609 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG C 610 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 249 through 270 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.307A pdb=" N TYR D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 312 " --> pdb=" O TYR D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 383 through 386 No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'D' and resid 396 through 420 removed outlier: 4.143A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 440 Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.204A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 484 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 326 through 345 removed outlier: 4.389A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 382 through 394 removed outlier: 4.213A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 434 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 464 through 474 removed outlier: 4.768A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 502 Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 562 Processing helix chain 'E' and resid 567 through 586 removed outlier: 5.595A pdb=" N ASP E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE E 586 " --> pdb=" O SER E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 593 through 610 removed outlier: 3.788A pdb=" N GLN E 608 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 156 through 159 No H-bonds generated for 'chain 'F' and resid 156 through 159' Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 219 through 232 Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 250 through 268 removed outlier: 3.937A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.273A pdb=" N TYR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 383 through 386 No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing helix chain 'F' and resid 396 through 424 removed outlier: 7.137A pdb=" N GLU F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLU F 423 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 442 Processing helix chain 'F' and resid 454 through 467 removed outlier: 4.071A pdb=" N ILE F 467 " --> pdb=" O SER F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 484 Processing helix chain 'G' and resid 76 through 113 removed outlier: 3.946A pdb=" N GLY G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 132 removed outlier: 3.777A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 5.446A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'H' and resid 64 through 103 removed outlier: 5.145A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 113 removed outlier: 3.600A pdb=" N THR I 48 " --> pdb=" O GLU I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 removed outlier: 3.586A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 163 removed outlier: 5.282A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'I' and resid 215 through 222 Processing helix chain 'J' and resid 6 through 62 Processing helix chain 'J' and resid 65 through 103 removed outlier: 3.543A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 112 removed outlier: 3.577A pdb=" N ASN K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix removed outlier: 3.531A pdb=" N ALA K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 removed outlier: 5.567A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 Processing helix chain 'K' and resid 215 through 223 Processing helix chain 'L' and resid 26 through 62 Processing helix chain 'L' and resid 68 through 90 removed outlier: 3.634A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 103 removed outlier: 3.823A pdb=" N ILE L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 75 Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 115 through 117 No H-bonds generated for 'chain 'M' and resid 115 through 117' Processing helix chain 'M' and resid 129 through 216 removed outlier: 4.991A pdb=" N ILE M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Proline residue: M 179 - end of helix Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 71 through 76 removed outlier: 3.767A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 Processing helix chain 'N' and resid 107 through 111 Processing helix chain 'P' and resid 11 through 22 Processing helix chain 'P' and resid 27 through 32 Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 74 through 86 removed outlier: 3.781A pdb=" N ILE P 78 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Proline residue: P 79 - end of helix Processing helix chain 'P' and resid 90 through 105 Processing helix chain 'P' and resid 111 through 119 Processing helix chain 'P' and resid 121 through 130 Processing helix chain 'P' and resid 136 through 151 Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 168 through 175 Processing helix chain 'P' and resid 180 through 195 removed outlier: 4.083A pdb=" N VAL P 195 " --> pdb=" O GLN P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 209 Processing helix chain 'P' and resid 211 through 222 Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 257 through 266 removed outlier: 3.527A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 280 Processing helix chain 'P' and resid 284 through 297 Processing helix chain 'P' and resid 305 through 315 Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 333 through 352 removed outlier: 3.736A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 372 through 375 No H-bonds generated for 'chain 'P' and resid 372 through 375' Processing helix chain 'P' and resid 377 through 410 removed outlier: 4.986A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP P 410 " --> pdb=" O VAL P 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 432 Processing helix chain 'P' and resid 435 through 443 removed outlier: 3.506A pdb=" N ASP P 439 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.783A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.625A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 96 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 removed outlier: 4.867A pdb=" N GLN A 140 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 162 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 172 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER A 160 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A 170 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.919A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.630A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU A 199 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER A 207 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU A 201 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.976A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 104 Processing sheet with id= H, first strand: chain 'B' and resid 112 through 114 removed outlier: 5.928A pdb=" N LEU B 240 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 328 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR B 276 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR B 330 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU B 278 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 357 through 359 Processing sheet with id= J, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.596A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 93 through 96 Processing sheet with id= L, first strand: chain 'C' and resid 139 through 141 Processing sheet with id= M, first strand: chain 'C' and resid 251 through 254 removed outlier: 8.204A pdb=" N THR C 252 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 412 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE C 254 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 414 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 301 through 303 removed outlier: 3.646A pdb=" N GLU C 309 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 396 through 399 removed outlier: 3.633A pdb=" N VAL C 410 " --> pdb=" O GLY C 396 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 157 through 161 removed outlier: 6.820A pdb=" N ILE C 172 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER C 160 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS C 170 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.693A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 185 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE C 197 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE C 209 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU C 199 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER C 207 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 26 through 28 removed outlier: 3.998A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 101 through 104 Processing sheet with id= T, first strand: chain 'D' and resid 111 through 113 removed outlier: 3.761A pdb=" N ARG D 111 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE D 210 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE D 241 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 171 through 173 Processing sheet with id= V, first strand: chain 'E' and resid 26 through 31 removed outlier: 6.516A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 86 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= X, first strand: chain 'E' and resid 189 through 191 removed outlier: 4.741A pdb=" N GLN E 140 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE E 172 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER E 160 " --> pdb=" O HIS E 170 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS E 170 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 409 through 414 removed outlier: 6.461A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP E 355 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL E 281 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.665A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE E 185 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 197 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 209 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU E 199 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER E 207 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.770A pdb=" N VAL E 399 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 31 through 35 removed outlier: 6.260A pdb=" N ILE F 40 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 101 through 104 Processing sheet with id= AD, first strand: chain 'F' and resid 357 through 360 removed outlier: 7.649A pdb=" N VAL F 360 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE F 173 " --> pdb=" O VAL F 360 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 209 through 211 removed outlier: 6.124A pdb=" N SER F 328 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR F 276 " --> pdb=" O SER F 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 330 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 213 through 217 removed outlier: 6.258A pdb=" N PHE F 241 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY F 216 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN F 243 " --> pdb=" O GLY F 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 171 through 174 Processing sheet with id= AH, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.978A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.973A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 92 through 97 Processing sheet with id= AK, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.533A pdb=" N ILE N 66 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA N 90 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE N 69 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU N 92 " --> pdb=" O ILE N 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1821 hydrogen bonds defined for protein. 5022 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: 13.10 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5160 1.30 - 1.43: 7748 1.43 - 1.55: 19112 1.55 - 1.68: 4 1.68 - 1.81: 163 Bond restraints: 32187 Sorted by residual: bond pdb=" CA TYR D 265 " pdb=" C TYR D 265 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.34e-02 5.57e+03 5.84e+01 bond pdb=" CA GLU A 47 " pdb=" C GLU A 47 " ideal model delta sigma weight residual 1.528 1.430 0.098 1.35e-02 5.49e+03 5.28e+01 bond pdb=" CA THR F 354 " pdb=" C THR F 354 " ideal model delta sigma weight residual 1.523 1.439 0.084 1.34e-02 5.57e+03 3.90e+01 bond pdb=" CA ALA B 165 " pdb=" C ALA B 165 " ideal model delta sigma weight residual 1.527 1.445 0.082 1.41e-02 5.03e+03 3.35e+01 bond pdb=" CA THR D 350 " pdb=" C THR D 350 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.30e-02 5.92e+03 3.00e+01 ... (remaining 32182 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.65: 757 105.65 - 113.19: 18024 113.19 - 120.74: 14691 120.74 - 128.28: 10503 128.28 - 135.83: 132 Bond angle restraints: 44107 Sorted by residual: angle pdb=" N GLU D 129 " pdb=" CA GLU D 129 " pdb=" C GLU D 129 " ideal model delta sigma weight residual 113.88 100.41 13.47 1.23e+00 6.61e-01 1.20e+02 angle pdb=" N ARG B 166 " pdb=" CA ARG B 166 " pdb=" C ARG B 166 " ideal model delta sigma weight residual 111.28 121.93 -10.65 1.09e+00 8.42e-01 9.55e+01 angle pdb=" N ASN C 288 " pdb=" CA ASN C 288 " pdb=" C ASN C 288 " ideal model delta sigma weight residual 111.28 104.92 6.36 1.09e+00 8.42e-01 3.41e+01 angle pdb=" N VAL L 95 " pdb=" CA VAL L 95 " pdb=" C VAL L 95 " ideal model delta sigma weight residual 109.34 98.48 10.86 2.08e+00 2.31e-01 2.73e+01 angle pdb=" N THR D 354 " pdb=" CA THR D 354 " pdb=" C THR D 354 " ideal model delta sigma weight residual 110.19 116.47 -6.28 1.24e+00 6.50e-01 2.56e+01 ... (remaining 44102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 18848 34.38 - 68.75: 250 68.75 - 103.13: 27 103.13 - 137.50: 0 137.50 - 171.88: 2 Dihedral angle restraints: 19127 sinusoidal: 5431 harmonic: 13696 Sorted by residual: dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 111.88 -171.88 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP A 702 " pdb=" O5' ADP A 702 " pdb=" PA ADP A 702 " pdb=" O2A ADP A 702 " ideal model delta sinusoidal sigma weight residual 300.00 130.37 169.64 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA THR E 315 " pdb=" C THR E 315 " pdb=" N THR E 316 " pdb=" CA THR E 316 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 19124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5063 0.086 - 0.172: 368 0.172 - 0.257: 8 0.257 - 0.343: 1 0.343 - 0.429: 2 Chirality restraints: 5442 Sorted by residual: chirality pdb=" CA ARG B 166 " pdb=" N ARG B 166 " pdb=" C ARG B 166 " pdb=" CB ARG B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE I 172 " pdb=" CA ILE I 172 " pdb=" CG1 ILE I 172 " pdb=" CG2 ILE I 172 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE C 167 " pdb=" CA ILE C 167 " pdb=" CG1 ILE C 167 " pdb=" CG2 ILE C 167 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5439 not shown) Planarity restraints: 5734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 417 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO C 418 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 418 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 418 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 348 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASP F 348 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP F 348 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU F 349 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 286 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ARG C 286 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 286 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 287 " 0.012 2.00e-02 2.50e+03 ... (remaining 5731 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 239 2.60 - 3.18: 28080 3.18 - 3.75: 52527 3.75 - 4.33: 68232 4.33 - 4.90: 116817 Nonbonded interactions: 265895 Sorted by model distance: nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 701 " model vdw 2.026 2.170 nonbonded pdb="MG MG A 701 " pdb=" O1B ADP A 702 " model vdw 2.072 2.170 nonbonded pdb=" O ASN E 39 " pdb=" ND2 ASN E 39 " model vdw 2.110 2.520 nonbonded pdb=" OE1 GLU B 129 " pdb=" OH TYR B 265 " model vdw 2.197 2.440 nonbonded pdb=" O ILE F 52 " pdb=" OG1 THR F 96 " model vdw 2.218 2.440 ... (remaining 265890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 65 or (resid 66 and (name N or nam \ e CA or name C or name O or name CB )) or resid 67 through 73 or (resid 74 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or r \ esid 84 through 101 or (resid 102 and (name N or name CA or name C or name O or \ name CB )) or resid 103 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 116 or (resid 117 th \ rough 121 and (name N or name CA or name C or name O or name CB )) or resid 122 \ through 129 or (resid 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 through 146 or (resid 147 through 148 and (name N or name CA or \ name C or name O or name CB )) or resid 149 or (resid 150 and (name N or name CA \ or name C or name O or name CB )) or resid 151 through 155 or (resid 156 and (n \ ame N or name CA or name C or name O or name CB )) or resid 157 through 176 or ( \ resid 177 through 178 and (name N or name CA or name C or name O or name CB )) o \ r resid 179 through 180 or (resid 181 and (name N or name CA or name C or name O \ or name CB )) or resid 182 or (resid 183 and (name N or name CA or name C or na \ me O or name CB )) or resid 184 through 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 198 or (resid 199 and (name N or name CA or name C or name O or name CB )) o \ r resid 200 through 205 or (resid 206 through 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 223 or (resid 224 through 225 an \ d (name N or name CA or name C or name O or name CB )) or resid 226 through 234 \ or (resid 235 and (name N or name CA or name C or name O or name CB )) or resid \ 236 through 240 or (resid 241 through 242 and (name N or name CA or name C or na \ me O or name CB )) or resid 243 through 257 or (resid 258 and (name N or name CA \ or name C or name O or name CB )) or resid 259 or (resid 260 and (name N or nam \ e CA or name C or name O or name CB )) or resid 261 or (resid 262 through 271 an \ d (name N or name CA or name C or name O or name CB )) or resid 272 or (resid 27 \ 3 through 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 288 or (resid 289 and (name N or name CA or name C or name O or name \ CB )) or resid 290 through 294 or (resid 295 through 296 and (name N or name CA \ or name C or name O or name CB )) or resid 297 through 301 or (resid 302 throug \ h 305 and (name N or name CA or name C or name O or name CB )) or (resid 306 thr \ ough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 o \ r (resid 311 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 12 through 314 or (resid 315 and (name N or name CA or name C or name O or name \ CB )) or resid 316 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 354 or (resid 355 through 358 and (na \ me N or name CA or name C or name O or name CB )) or resid 359 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 367 or (resid 368 and (name N or name CA or name C or name O \ or name CB )) or resid 369 through 377 or (resid 378 and (name N or name CA or n \ ame C or name O or name CB )) or resid 379 through 389 or (resid 390 and (name N \ or name CA or name C or name O or name CB )) or resid 391 through 417 or resid \ 425 through 442 or (resid 443 through 444 and (name N or name CA or name C or na \ me O or name CB )) or resid 445 through 446 or (resid 447 through 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 452 or (resi \ d 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or ( \ resid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 \ through 457 or (resid 458 through 459 and (name N or name CA or name C or name O \ or name CB )) or resid 460 through 464 or (resid 465 and (name N or name CA or \ name C or name O or name CB )) or resid 466 through 467 or (resid 468 through 46 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 470 through \ 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) or re \ sid 475 through 483 or (resid 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 through 490 or (resid 491 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 512 and (name N or \ name CA or name C or name O or name CB )) or resid 513 through 514 or (resid 515 \ through 516 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 17 through 528 or (resid 529 and (name N or name CA or name C or name O or name \ CB )) or resid 530 or (resid 531 through 533 and (name N or name CA or name C or \ name O or name CB )) or resid 534 through 537 or (resid 538 and (name N or name \ CA or name C or name O or name CB )) or resid 539 through 544 or (resid 545 and \ (name N or name CA or name C or name O or name CB )) or resid 546 through 557 o \ r (resid 558 through 563 and (name N or name CA or name C or name O or name CB ) \ ) or resid 564 through 569 or (resid 570 through 574 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 575 through 580 and (name N or name CA o \ r name C or name O or name CB )) or resid 581 through 583 or (resid 584 through \ 585 and (name N or name CA or name C or name O or name CB )) or resid 586 throug \ h 587 or (resid 588 and (name N or name CA or name C or name O or name CB )) or \ resid 589 through 590 or (resid 591 and (name N or name CA or name C or name O o \ r name CB )) or resid 592 through 602 or (resid 603 through 613 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 35 or (resid 36 through 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thr \ ough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 73 or (resid 74 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 through 82 or (resid 83 and (name N or name CA \ or name C or name O or name CB )) or resid 84 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 107 or (resi \ d 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thro \ ugh 118 or (resid 119 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 through 129 or (resid 130 and (name N or name CA or name \ C or name O or name CB )) or resid 131 through 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 159 or (resid 16 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 176 or (resid 177 through 178 and (name N or name CA or name C or name O or name \ CB )) or resid 179 through 180 or (resid 181 and (name N or name CA or name C o \ r name O or name CB )) or resid 182 or (resid 183 and (name N or name CA or name \ C or name O or name CB )) or resid 184 through 194 or (resid 195 through 196 an \ d (name N or name CA or name C or name O or name CB )) or resid 197 through 204 \ or (resid 205 through 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 223 or (resid 224 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 through 234 or (resid 235 and (name \ N or name CA or name C or name O or name CB )) or resid 236 through 250 or (resi \ d 251 and (name N or name CA or name C or name O or name CB )) or resid 252 thro \ ugh 261 or (resid 262 through 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 273 or (resid 274 through 277 and (name N or nam \ e CA or name C or name O or name CB )) or resid 278 through 291 or (resid 292 an \ d (name N or name CA or name C or name O or name CB )) or resid 293 through 321 \ or (resid 322 and (name N or name CA or name C or name O or name CB )) or resid \ 323 through 410 or (resid 411 and (name N or name CA or name C or name O or name \ CB )) or resid 412 through 415 or (resid 416 through 417 and (name N or name CA \ or name C or name O or name CB )) or resid 425 through 452 or (resid 453 and (n \ ame N or name CA or name C or name O or name CB )) or resid 454 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 537 or (resid 538 and (name N or name CA or name C or name O \ or name CB )) or resid 539 through 613)) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 through 35 or (resid 36 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or \ name CA or name C or name O or name CB )) or resid 42 or (resid 43 through 44 an \ d (name N or name CA or name C or name O or name CB )) or resid 45 through 50 or \ (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 \ through 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 through 58 or (resid 59 and (name N or name CA or name C or name O \ or name CB )) or resid 60 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 107 or (resid 108 and (name N or \ name CA or name C or name O or name CB )) or resid 109 through 133 or (resid 134 \ and (name N or name CA or name C or name O or name CB )) or resid 135 through 2 \ 05 or (resid 206 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 250 or (resid 251 and (name N or name CA or name C or \ name O or name CB )) or resid 252 through 275 or (resid 276 through 277 and (na \ me N or name CA or name C or name O or name CB )) or resid 278 through 284 or (r \ esid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 t \ hrough 288 or (resid 289 and (name N or name CA or name C or name O or name CB ) \ ) or resid 290 through 301 or (resid 302 through 305 and (name N or name CA or n \ ame C or name O or name CB )) or resid 306 through 310 or (resid 311 and (name N \ or name CA or name C or name O or name CB )) or resid 312 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 329 or (resid 330 through 332 and (name N or name CA or name \ C or name O or name CB )) or resid 333 through 350 or (resid 351 and (name N or \ name CA or name C or name O or name CB )) or resid 352 through 356 or (resid 357 \ through 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 361 or (resid 362 through 363 and (name N or name CA or name C or nam \ e O or name CB )) or resid 364 through 365 or (resid 366 and (name N or name CA \ or name C or name O or name CB )) or resid 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 377 or (resid 378 and \ (name N or name CA or name C or name O or name CB )) or resid 379 through 404 o \ r (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 06 or (resid 407 and (name N or name CA or name C or name O or name CB )) or res \ id 408 through 415 or (resid 416 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 through 446 or (resid 447 through 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 through 454 or (r \ esid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 t \ hrough 458 or (resid 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 467 or (resid 468 through 469 and (name N or name CA or n \ ame C or name O or name CB )) or resid 470 through 482 or (resid 483 through 484 \ and (name N or name CA or name C or name O or name CB )) or resid 485 through 4 \ 90 or (resid 491 through 502 and (name N or name CA or name C or name O or name \ CB )) or (resid 503 through 512 and (name N or name CA or name C or name O or na \ me CB )) or resid 513 through 514 or (resid 515 through 516 and (name N or name \ CA or name C or name O or name CB )) or resid 517 through 530 or (resid 531 thro \ ugh 533 and (name N or name CA or name C or name O or name CB )) or resid 534 th \ rough 557 or (resid 558 through 563 and (name N or name CA or name C or name O o \ r name CB )) or resid 564 through 569 or (resid 570 through 574 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 575 through 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 or (resid 582 through 5 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 586 through \ 589 or (resid 590 through 591 and (name N or name CA or name C or name O or nam \ e CB )) or resid 592 through 602 or (resid 603 through 613 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 17 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 98 or (resid 99 and ( \ name N or name CA or name C or name O or name CB )) or resid 100 through 105 or \ (resid 106 through 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 120 or (resid 121 through 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 136 or (resid 137 and (name N o \ r name CA or name C or name O or name CB )) or resid 138 through 147 or (resid 1 \ 48 through 149 and (name N or name CA or name C or name O or name CB )) or resid \ 150 through 151 or (resid 152 and (name N or name CA or name C or name O or nam \ e CB )) or resid 153 through 155 or (resid 156 through 157 and (name N or name C \ A or name C or name O or name CB )) or resid 158 through 161 or (resid 162 throu \ gh 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thr \ ough 194 or (resid 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 or (resid 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB )) or resid 219 through 220 or (resid 221 through 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 225 or (res \ id 226 through 228 and (name N or name CA or name C or name O or name CB )) or r \ esid 229 or (resid 230 through 232 and (name N or name CA or name C or name O or \ name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 237 or (resid 238 through 239 and (name N o \ r name CA or name C or name O or name CB )) or resid 240 through 245 or (resid 2 \ 46 through 247 and (name N or name CA or name C or name O or name CB )) or resid \ 248 through 250 or (resid 251 and (name N or name CA or name C or name O or nam \ e CB )) or resid 252 through 263 or (resid 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 270 or (resid 271 and (name N or na \ me CA or name C or name O or name CB )) or resid 272 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB )) or resid 284 through 285 \ or (resid 286 through 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 312 or (resid 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 316 or \ (resid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 \ through 325 or (resid 326 and (name N or name CA or name C or name O or name CB \ )) or resid 327 through 333 or (resid 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 340 or (resid 341 and (name N or name C \ A or name C or name O or name CB )) or resid 342 or (resid 343 and (name N or na \ me CA or name C or name O or name CB )) or resid 344 through 377 or (resid 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 through \ 383 or (resid 384 through 387 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 388 through 392 and (name N or name CA or name C or name O or \ name CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name \ C or name O or name CB )) or resid 396 through 399 or (resid 400 through 401 an \ d (name N or name CA or name C or name O or name CB )) or resid 402 through 415 \ or (resid 416 through 420 and (name N or name CA or name C or name O or name CB \ )) or (resid 421 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or name C or \ name O or name CB )) or resid 439 through 440 or (resid 441 through 442 and (na \ me N or name CA or name C or name O or name CB )) or resid 443 through 455 or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 t \ hrough 458 or (resid 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 469 or (resid 470 through 472 and (name N or name CA or n \ ame C or name O or name CB )) or resid 473 or (resid 474 and (name N or name CA \ or name C or name O or name CB )) or resid 475 through 476 or (resid 477 and (na \ me N or name CA or name C or name O or name CB )) or resid 478 through 485)) selection = (chain 'D' and (resid 17 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 50 or (resid 51 throu \ gh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or r \ esid 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or \ resid 74 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB )) or resid 126 through 148 or (resid 149 and (name N \ or name CA or name C or name O or name CB )) or resid 150 through 151 or (resid \ 152 and (name N or name CA or name C or name O or name CB )) or resid 153 throug \ h 155 or (resid 156 through 157 and (name N or name CA or name C or name O or na \ me CB )) or resid 158 through 161 or (resid 162 through 163 and (name N or name \ CA or name C or name O or name CB )) or resid 164 through 220 or (resid 221 thro \ ugh 222 and (name N or name CA or name C or name O or name CB )) or resid 223 th \ rough 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) \ or resid 233 through 237 or (resid 238 through 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 245 or (resid 246 through 247 \ and (name N or name CA or name C or name O or name CB )) or resid 248 through 26 \ 3 or (resid 264 and (name N or name CA or name C or name O or name CB )) or resi \ d 265 through 316 or (resid 317 and (name N or name CA or name C or name O or na \ me CB )) or resid 318 through 384 or (resid 385 through 387 and (name N or name \ CA or name C or name O or name CB )) or (resid 388 through 392 and (name N or na \ me CA or name C or name O or name CB )) or resid 393 or (resid 394 through 395 a \ nd (name N or name CA or name C or name O or name CB )) or resid 396 through 415 \ or (resid 416 through 420 and (name N or name CA or name C or name O or name CB \ )) or (resid 421 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or name C o \ r name O or name CB )) or resid 439 through 440 or (resid 441 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or resid 443 through 455 or ( \ resid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ through 482 or (resid 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 485)) selection = (chain 'F' and ((resid 17 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 42 or (resid 43 and (name N or na \ me CA or name C or name O or name CB )) or resid 44 through 50 or (resid 51 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or \ resid 62 through 117 or (resid 118 and (name N or name CA or name C or name O or \ name CB )) or resid 119 through 120 or (resid 121 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 208 or (resid 209 a \ nd (name N or name CA or name C or name O or name CB )) or resid 210 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 225 or (resid 226 through 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 289 or (resid 290 and ( \ name N or name CA or name C or name O or name CB )) or resid 291 through 296 or \ (resid 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ through 322 or (resid 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 through 333 or (resid 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 338 or (resid 339 through 341 and (name \ N or name CA or name C or name O or name CB )) or resid 342 through 347 or (res \ id 348 and (name N or name CA or name C or name O or name CB )) or resid 349 thr \ ough 391 or (resid 392 and (name N or name CA or name C or name O or name CB )) \ or resid 393 through 400 or (resid 401 and (name N or name CA or name C or name \ O or name CB )) or resid 402 through 458 or (resid 459 and (name N or name CA or \ name C or name O or name CB )) or resid 460 through 469 or (resid 470 through 4 \ 72 and (name N or name CA or name C or name O or name CB )) or resid 473 or (res \ id 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thr \ ough 485)) } ncs_group { reference = (chain 'I' and (resid 27 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 102 or (resid 103 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thr \ ough 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) \ or resid 124 through 133 or (resid 134 and (name N or name CA or name C or name \ O or name CB )) or resid 135 through 183 or (resid 184 through 185 and (name N o \ r name CA or name C or name O or name CB )) or resid 186 through 193 or (resid 1 \ 94 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 210 or (resid 211 through 214 and (name N or name CA or name C or n \ ame O or name CB )) or resid 215 through 227 or (resid 228 and (name N or name C \ A or name C or name O or name CB )) or resid 229 or (resid 230 and (name N or na \ me CA or name C or name O or name CB )) or resid 231)) selection = (chain 'K' and (resid 27 through 77 or (resid 78 through 85 and (name N or name \ CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N or nam \ e CA or name C or name O or name CB )) or resid 88 through 94 or (resid 95 and ( \ name N or name CA or name C or name O or name CB )) or resid 96 through 105 or ( \ resid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ through 109 or (resid 110 through 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 126 or (resid 127 through 128 and (name N or \ name CA or name C or name O or name CB )) or resid 129 through 164 or (resid 16 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 166 through \ 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 90 5.16 5 C 20279 2.51 5 N 5709 2.21 5 O 5561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.040 Extract box with map and model: 16.700 Check model and map are aligned: 0.470 Process input model: 84.270 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.004 0.102 32187 Z= 0.280 Angle : 0.573 13.475 44107 Z= 0.321 Chirality : 0.043 0.429 5442 Planarity : 0.004 0.055 5734 Dihedral : 12.666 171.880 10287 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.29 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % 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: 1.28 (0.13), residues: 4694 helix: 2.30 (0.11), residues: 2343 sheet: -1.64 (0.22), residues: 548 loop : -0.23 (0.15), residues: 1803 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 416 time to evaluate : 3.860 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 421 average time/residue: 0.5159 time to fit residues: 342.9636 Evaluate side-chains 373 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 369 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3027 time to fit residues: 7.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 141 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 527 GLN C 164 ASN C 323 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 164 ASN E 346 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 ASN M 153 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 32187 Z= 0.391 Angle : 0.577 7.918 44107 Z= 0.300 Chirality : 0.045 0.234 5442 Planarity : 0.005 0.049 5734 Dihedral : 5.495 173.074 5049 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 4694 helix: 2.14 (0.11), residues: 2320 sheet: -1.82 (0.21), residues: 546 loop : -0.24 (0.15), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 363 time to evaluate : 3.978 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 383 average time/residue: 0.4914 time to fit residues: 295.6347 Evaluate side-chains 361 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 343 time to evaluate : 3.981 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3457 time to fit residues: 16.8192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 chunk 288 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 424 optimal weight: 50.0000 chunk 458 optimal weight: 6.9990 chunk 378 optimal weight: 0.0570 chunk 421 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 340 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 323 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 29 ASN F 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 32187 Z= 0.274 Angle : 0.512 6.770 44107 Z= 0.265 Chirality : 0.043 0.317 5442 Planarity : 0.004 0.046 5734 Dihedral : 5.225 167.281 5049 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.11 (0.13), residues: 4694 helix: 2.19 (0.11), residues: 2311 sheet: -1.97 (0.20), residues: 569 loop : -0.19 (0.15), residues: 1814 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 377 time to evaluate : 3.804 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 391 average time/residue: 0.4945 time to fit residues: 308.6699 Evaluate side-chains 364 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 350 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3299 time to fit residues: 14.0103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 40.0000 chunk 319 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 285 optimal weight: 0.0980 chunk 426 optimal weight: 50.0000 chunk 451 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 404 optimal weight: 50.0000 chunk 121 optimal weight: 0.3980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN D 331 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 164 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 32187 Z= 0.412 Angle : 0.570 7.958 44107 Z= 0.294 Chirality : 0.045 0.302 5442 Planarity : 0.005 0.048 5734 Dihedral : 5.319 165.236 5049 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.93 (0.13), residues: 4694 helix: 2.04 (0.11), residues: 2319 sheet: -2.08 (0.20), residues: 563 loop : -0.28 (0.15), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 3.851 Fit side-chains outliers start: 47 outliers final: 26 residues processed: 384 average time/residue: 0.5107 time to fit residues: 316.0061 Evaluate side-chains 365 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 339 time to evaluate : 3.751 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3476 time to fit residues: 22.3674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 336 optimal weight: 40.0000 chunk 186 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 405 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 32187 Z= 0.313 Angle : 0.524 7.091 44107 Z= 0.270 Chirality : 0.043 0.297 5442 Planarity : 0.004 0.047 5734 Dihedral : 5.130 159.899 5049 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.13), residues: 4694 helix: 2.09 (0.11), residues: 2316 sheet: -2.07 (0.20), residues: 563 loop : -0.25 (0.15), residues: 1815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 360 time to evaluate : 4.075 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 379 average time/residue: 0.4883 time to fit residues: 295.1962 Evaluate side-chains 357 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 341 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4066 time to fit residues: 16.5412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 451 optimal weight: 7.9990 chunk 375 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 237 optimal weight: 0.0970 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 186 GLN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 32187 Z= 0.293 Angle : 0.520 8.070 44107 Z= 0.267 Chirality : 0.043 0.295 5442 Planarity : 0.004 0.047 5734 Dihedral : 5.014 155.327 5049 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.13), residues: 4694 helix: 2.13 (0.11), residues: 2314 sheet: -2.05 (0.20), residues: 560 loop : -0.24 (0.15), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 352 time to evaluate : 3.787 Fit side-chains outliers start: 24 outliers final: 7 residues processed: 367 average time/residue: 0.5053 time to fit residues: 294.5432 Evaluate side-chains 349 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 342 time to evaluate : 3.580 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2801 time to fit residues: 8.8848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 329 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 450 optimal weight: 10.0000 chunk 281 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 274 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 339 ASN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 32187 Z= 0.278 Angle : 0.509 7.561 44107 Z= 0.262 Chirality : 0.043 0.260 5442 Planarity : 0.004 0.047 5734 Dihedral : 4.900 153.313 5049 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.06 (0.13), residues: 4694 helix: 2.15 (0.11), residues: 2308 sheet: -1.98 (0.21), residues: 555 loop : -0.23 (0.15), residues: 1831 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 355 time to evaluate : 3.842 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 372 average time/residue: 0.4993 time to fit residues: 296.6275 Evaluate side-chains 360 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 344 time to evaluate : 3.765 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3219 time to fit residues: 15.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 268 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 353 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 32187 Z= 0.211 Angle : 0.486 8.106 44107 Z= 0.250 Chirality : 0.042 0.202 5442 Planarity : 0.004 0.046 5734 Dihedral : 4.759 162.034 5049 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.20 (0.13), residues: 4694 helix: 2.26 (0.11), residues: 2314 sheet: -1.83 (0.21), residues: 560 loop : -0.17 (0.15), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 365 time to evaluate : 3.905 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 373 average time/residue: 0.5086 time to fit residues: 302.9680 Evaluate side-chains 347 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 343 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3117 time to fit residues: 7.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 0.5980 chunk 431 optimal weight: 8.9990 chunk 393 optimal weight: 2.9990 chunk 419 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 329 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 396 optimal weight: 9.9990 chunk 417 optimal weight: 0.0010 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 164 ASN F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 32187 Z= 0.268 Angle : 0.510 10.129 44107 Z= 0.262 Chirality : 0.042 0.262 5442 Planarity : 0.004 0.048 5734 Dihedral : 4.863 175.900 5049 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.19 (0.13), residues: 4694 helix: 2.25 (0.11), residues: 2309 sheet: -1.81 (0.21), residues: 555 loop : -0.19 (0.15), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 355 time to evaluate : 4.030 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 360 average time/residue: 0.4956 time to fit residues: 285.2507 Evaluate side-chains 360 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 3.681 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3549 time to fit residues: 11.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 0.2980 chunk 443 optimal weight: 50.0000 chunk 270 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 465 optimal weight: 7.9990 chunk 428 optimal weight: 0.0970 chunk 370 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 32187 Z= 0.223 Angle : 0.493 8.895 44107 Z= 0.254 Chirality : 0.042 0.212 5442 Planarity : 0.004 0.048 5734 Dihedral : 4.750 169.101 5049 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.26 (0.13), residues: 4694 helix: 2.30 (0.11), residues: 2300 sheet: -1.75 (0.21), residues: 549 loop : -0.15 (0.15), residues: 1845 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 354 time to evaluate : 3.828 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 358 average time/residue: 0.4974 time to fit residues: 282.4171 Evaluate side-chains 350 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 3.619 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3217 time to fit residues: 7.4332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 0.7980 chunk 394 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 341 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 381 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 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 = 0.3642 r_free = 0.3642 target = 0.148004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113887 restraints weight = 38971.167| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.78 r_work: 0.2980 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 32187 Z= 0.237 Angle : 0.499 10.429 44107 Z= 0.256 Chirality : 0.042 0.244 5442 Planarity : 0.004 0.048 5734 Dihedral : 4.650 155.628 5049 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.25 (0.13), residues: 4694 helix: 2.30 (0.11), residues: 2300 sheet: -1.75 (0.21), residues: 555 loop : -0.17 (0.15), residues: 1839 =============================================================================== Job complete usr+sys time: 6827.87 seconds wall clock time: 124 minutes 43.61 seconds (7483.61 seconds total)