Starting phenix.real_space_refine (version: dev) on Tue Feb 28 02:35:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmo_25997/02_2023/7tmo_25997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmo_25997/02_2023/7tmo_25997.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/7tmo_25997/02_2023/7tmo_25997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmo_25997/02_2023/7tmo_25997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmo_25997/02_2023/7tmo_25997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmo_25997/02_2023/7tmo_25997_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= 0.126 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 GLU 47": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "L GLU 100": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31559 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4285 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 23, 'GLU:plan': 25, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3390 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 22, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 189 Chain: "C" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 3690 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 554} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1073 Unresolved non-hydrogen dihedrals: 704 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 10, 'GLU:plan': 38, 'ASP:plan': 31} Unresolved non-hydrogen planarities: 513 Chain: "D" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3306 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ASN:plan1': 10, 'ARG:plan': 3, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 215 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4113 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 7, 'ASP:plan': 27, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 298 Chain: "F" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3317 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 30, 'ARG:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 211 Chain: "G" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1273 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 5, 'TRANS': 194} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "H" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 456 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 90 Chain: "I" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1326 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 249 Chain: "J" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 570 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 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': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1308 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 213 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: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1235 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 300 Chain: "N" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 283 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: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2193 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1426 Unresolved non-hydrogen angles: 1821 Unresolved non-hydrogen dihedrals: 1158 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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: 17.93, per 1000 atoms: 0.57 Number of scatterers: 31559 At special positions: 0 Unit cell: (142.14, 165.83, 185.4, 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 82 16.00 P 5 15.00 Mg 2 11.99 O 5642 8.00 N 5698 7.00 C 20130 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: 13.04 Conformation dependent library (CDL) restraints added in 5.3 seconds 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8998 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 37 sheets defined 49.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 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 Processing helix chain 'A' and resid 287 through 296 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 345 removed outlier: 3.782A 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 426 through 434 Processing helix chain 'A' and resid 443 through 449 removed outlier: 4.493A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.582A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 3.885A 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 563 Processing helix chain 'A' and resid 567 through 586 removed outlier: 5.697A pdb=" N ASP A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) 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 612 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 160 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 268 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.498A 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 367 Processing helix chain 'B' and resid 396 through 420 Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 454 through 467 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 265 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 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 326 through 346 removed outlier: 4.894A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' 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 474 removed outlier: 4.522A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 501 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 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 540 through 563 Processing helix chain 'C' and resid 567 through 586 removed outlier: 5.288A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 614 removed outlier: 3.694A pdb=" N HIS C 597 " --> pdb=" O GLU C 593 " (cutoff:3.500A) 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 231 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 295 removed outlier: 3.822A pdb=" N ARG D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.021A pdb=" N TYR D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 312 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 317 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' 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: 4.192A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 441 removed outlier: 3.578A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.447A 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 243 Processing helix chain 'E' and resid 262 through 271 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: 3.931A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.059A 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: 4.266A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' 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 473 removed outlier: 4.825A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.494A 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 563 Processing helix chain 'E' and resid 567 through 585 removed outlier: 5.637A pdb=" N ASP E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 612 removed outlier: 6.761A pdb=" N GLU E 593 " --> pdb=" O SER E 590 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS E 594 " --> pdb=" O ARG E 591 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 595 " --> pdb=" O GLY E 592 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS E 597 " --> pdb=" O LYS E 594 " (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 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 250 through 269 removed outlier: 3.997A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix removed outlier: 3.537A pdb=" N TYR F 268 " --> pdb=" O TYR F 265 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN F 269 " --> pdb=" O LEU F 266 " (cutoff:3.500A) 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 308 through 318 removed outlier: 4.061A pdb=" N ARG F 318 " --> pdb=" O THR F 314 " (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 419 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 427 through 441 Processing helix chain 'F' and resid 454 through 467 removed outlier: 4.144A 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 33 through 113 removed outlier: 3.568A pdb=" N ILE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 132 removed outlier: 3.513A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 163 removed outlier: 4.618A pdb=" N ASP G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.556A 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 223 Processing helix chain 'H' and resid 33 through 60 Processing helix chain 'H' and resid 64 through 102 removed outlier: 4.195A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 113 removed outlier: 3.699A pdb=" N GLU I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 130 removed outlier: 4.015A pdb=" N VAL I 126 " --> pdb=" O GLN I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 163 removed outlier: 5.477A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 222 removed outlier: 3.677A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Proline residue: I 216 - end of helix Processing helix chain 'J' and resid 6 through 62 removed outlier: 3.912A pdb=" N ALA J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 103 removed outlier: 3.667A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 112 removed outlier: 3.909A pdb=" N ARG K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix removed outlier: 3.873A pdb=" N ALA K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 163 removed outlier: 3.646A pdb=" N VAL K 146 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP K 147 " --> pdb=" O ARG K 144 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS K 153 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP K 154 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 163 " --> pdb=" O TYR K 160 " (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 67 removed outlier: 3.592A pdb=" N LYS L 33 " --> pdb=" O GLN L 29 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA L 40 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY L 64 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 103 removed outlier: 3.858A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (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 129 through 216 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: 3.730A 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 removed outlier: 3.609A pdb=" N ARG N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) No H-bonds generated for '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 51 Processing helix chain 'P' and resid 74 through 86 removed outlier: 3.589A 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: 4.116A 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: 3.617A 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 298 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: 3.745A 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: 5.042A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.709A 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: 4.395A 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 Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.781A 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: 6.726A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.915A 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: 6.799A pdb=" N ILE A 172 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 160 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS A 170 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 205 through 209 removed outlier: 6.118A pdb=" N GLU A 201 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 182 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 350 through 354 removed outlier: 7.110A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.874A pdb=" N GLU B 69 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 78 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 67 " --> pdb=" O GLN B 78 " (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 171 through 173 Processing sheet with id= I, first strand: chain 'B' and resid 320 through 322 removed outlier: 3.673A pdb=" N ILE B 329 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 322 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B 327 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 278 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER B 209 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE B 277 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 211 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 279 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 213 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 241 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 216 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ASN B 243 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.419A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.061A 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 189 through 192 removed outlier: 6.831A pdb=" N ILE C 172 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER C 160 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS C 170 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 251 through 254 removed outlier: 8.020A pdb=" N THR C 252 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 412 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 254 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 414 " --> pdb=" O ILE C 254 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 278 through 280 Processing sheet with id= O, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.560A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 223 through 226 removed outlier: 6.900A pdb=" N VAL C 399 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 26 through 28 removed outlier: 3.985A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 66 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 101 through 104 Processing sheet with id= S, first strand: chain 'D' and resid 171 through 173 Processing sheet with id= T, first strand: chain 'D' and resid 212 through 214 removed outlier: 6.070A pdb=" N ILE D 277 " --> pdb=" O ALA D 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 68 through 71 removed outlier: 5.416A pdb=" N GLU E 38 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE E 27 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.590A 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 139 through 141 Processing sheet with id= Y, first strand: chain 'E' and resid 207 through 209 Processing sheet with id= Z, first strand: chain 'E' and resid 251 through 253 removed outlier: 7.808A pdb=" N THR E 252 " --> pdb=" O VAL E 410 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 412 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 278 through 281 Processing sheet with id= AB, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.580A pdb=" N LEU F 41 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.666A 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 removed outlier: 3.525A pdb=" N LEU F 132 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 151 through 153 removed outlier: 4.080A pdb=" N GLY F 192 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 357 through 359 Processing sheet with id= AF, first strand: chain 'F' and resid 274 through 279 removed outlier: 6.766A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE F 277 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 211 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR F 279 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA F 213 " --> pdb=" O THR F 279 " (cutoff:3.500A) 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 138 through 141 removed outlier: 3.549A pdb=" N LYS I 140 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL I 189 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.058A 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 98 Processing sheet with id= AK, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.344A pdb=" N ILE N 66 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA N 90 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE N 69 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU N 92 " --> pdb=" O ILE N 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1861 hydrogen bonds defined for protein. 5217 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: 12.29 Time building geometry restraints manager: 13.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10697 1.34 - 1.46: 4000 1.46 - 1.57: 17214 1.57 - 1.69: 8 1.69 - 1.81: 148 Bond restraints: 32067 Sorted by residual: bond pdb=" CA THR E 88 " pdb=" CB THR E 88 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.56e-02 4.11e+03 2.56e+00 bond pdb=" CA THR E 88 " pdb=" C THR E 88 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.30e-02 5.92e+03 1.88e+00 bond pdb=" C LEU D 376 " pdb=" N PRO D 377 " ideal model delta sigma weight residual 1.336 1.348 -0.012 9.80e-03 1.04e+04 1.58e+00 bond pdb=" N THR E 88 " pdb=" CA THR E 88 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.21e-02 6.83e+03 1.29e+00 bond pdb=" CG1 ILE F 315 " pdb=" CD1 ILE F 315 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.26e+00 ... (remaining 32062 not shown) Histogram of bond angle deviations from ideal: 98.54 - 106.79: 909 106.79 - 115.04: 19246 115.04 - 123.29: 22982 123.29 - 131.54: 839 131.54 - 139.78: 28 Bond angle restraints: 44004 Sorted by residual: angle pdb=" N ILE B 120 " pdb=" CA ILE B 120 " pdb=" C ILE B 120 " ideal model delta sigma weight residual 111.91 107.46 4.45 8.90e-01 1.26e+00 2.50e+01 angle pdb=" N MET F 161 " pdb=" CA MET F 161 " pdb=" CB MET F 161 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 angle pdb=" C LYS D 367 " pdb=" N GLY D 368 " pdb=" CA GLY D 368 " ideal model delta sigma weight residual 122.16 119.44 2.72 7.70e-01 1.69e+00 1.25e+01 angle pdb=" N THR E 88 " pdb=" CA THR E 88 " pdb=" C THR E 88 " ideal model delta sigma weight residual 111.28 114.86 -3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" N GLY D 368 " pdb=" CA GLY D 368 " pdb=" C GLY D 368 " ideal model delta sigma weight residual 111.16 116.56 -5.40 1.76e+00 3.23e-01 9.40e+00 ... (remaining 43999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 18512 28.54 - 57.09: 441 57.09 - 85.63: 24 85.63 - 114.17: 7 114.17 - 142.71: 2 Dihedral angle restraints: 18986 sinusoidal: 5056 harmonic: 13930 Sorted by residual: dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 157.29 142.71 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.17 -122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " pdb=" PA ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.00 -98.00 1 2.00e+01 2.50e-03 2.73e+01 ... (remaining 18983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4241 0.045 - 0.090: 959 0.090 - 0.136: 273 0.136 - 0.181: 11 0.181 - 0.226: 5 Chirality restraints: 5489 Sorted by residual: chirality pdb=" CB ILE E 108 " pdb=" CA ILE E 108 " pdb=" CG1 ILE E 108 " pdb=" CG2 ILE E 108 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+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 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 5486 not shown) Planarity restraints: 5734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 178 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO M 179 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 179 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 179 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 174 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C GLU M 174 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU M 174 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS M 175 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 477 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 478 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.033 5.00e-02 4.00e+02 ... (remaining 5731 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 115 2.53 - 3.12: 24948 3.12 - 3.72: 52166 3.72 - 4.31: 66699 4.31 - 4.90: 115797 Nonbonded interactions: 259725 Sorted by model distance: nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 702 " model vdw 1.942 2.170 nonbonded pdb=" O1G ATP A 701 " pdb="MG MG A 702 " model vdw 1.988 2.170 nonbonded pdb=" OG1 THR E 263 " pdb="MG MG E 702 " model vdw 2.053 2.170 nonbonded pdb=" NH1 ARG G 206 " pdb=" O VAL H 102 " model vdw 2.199 2.520 nonbonded pdb=" O LYS B 438 " pdb=" OG1 THR B 442 " model vdw 2.211 2.440 ... (remaining 259720 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 37 or (resid 38 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 49 or (resid 50 through \ 51 and (name N or name CA or name C or name O or name CB )) or resid 52 through \ 53 or (resid 54 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 65 or (resid 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 through 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 89 or (resid 90 and (name N o \ r name CA or name C or name O or name CB )) or resid 91 through 100 or (resid 10 \ 1 through 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 name CA or name C or na \ me O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name CA \ or name C or name O or name CB )) or resid 120 through 129 or (resid 130 and (n \ ame N or name CA or name C or name O or name CB )) or resid 131 through 135 or ( \ resid 136 and (name N or name CA or name C or name O or name CB )) or resid 137 \ or (resid 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or re \ sid 141 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 or (resid 150 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 through 163 or (resid 16 \ 4 through 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 or (resid 168 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 178 or (resid 179 and (name N or name CA or name C o \ r name O or name CB )) or resid 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 name 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 or (resid 192 and (n \ ame N or name CA or name C or name O or name CB )) or resid 193 or (resid 194 th \ rough 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 198 or (resid 199 and (name N or name CA or name C or name O or name CB \ )) or resid 200 or (resid 201 through 203 and (name N or name CA or name C or na \ me O or name CB )) or (resid 204 through 208 and (name N or name CA or name C or \ name O or name CB )) or resid 209 or (resid 210 and (name N or name CA or name \ C or name O or name CB )) or resid 211 through 223 or (resid 224 through 226 and \ (name N or name CA or name C or name O or name CB )) or resid 227 through 234 o \ r (resid 235 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 36 or (resid 237 through 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or name C or \ name O or name CB )) or resid 244 through 256 or (resid 264 through 268 and (na \ me N or name CA or name C or name O or name CB )) or resid 269 or (resid 270 thr \ ough 271 and (name N or name CA or name C or name O or name CB )) or resid 272 o \ r (resid 273 through 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 282 or (resid 283 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 284 through 286 and (name N or name CA or name C or \ name O or name CB )) or resid 287 or (resid 288 through 305 and (name N or name \ CA or name C or name O or name CB )) or (resid 306 through 311 and (name N or na \ me CA or name C or name O or name CB )) or resid 312 or (resid 313 and (name N o \ r name CA or name C or name O or name CB )) or resid 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 319 or (res \ id 320 and (name N or name CA or name C or name O or name CB )) or resid 321 thr \ ough 329 or (resid 330 through 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 350 or (resid 351 and (name N or name CA or nam \ e C or name O or name CB )) or resid 352 through 354 or (resid 355 through 357 a \ nd (name N or name CA or name C or name O or name CB )) or resid 358 or (resid 3 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 361 or (resid 362 through 363 and (name N or name CA or name C or name O or nam \ e 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 372 or (resid 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 377 or (resid 378 a \ nd (name N or name CA or name 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 392 or (resid 393 and (name N or name CA or name C or name O or nam \ e CB )) or resid 394 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 or (resid 409 and (name N or name CA or \ name C or name O or name CB )) or resid 410 through 416 or (resid 417 through 4 \ 19 and (name N or name CA or name C or name O or name CB )) or (resid 420 throug \ h 425 and (name N or name CA or name C or name O or name CB )) or resid 426 or ( \ resid 427 through 430 and (name N or name CA or name C or name O or name CB )) o \ r resid 431 through 440 or (resid 441 through 451 and (name N or name CA or name \ C or name O or name CB )) or resid 452 or (resid 453 through 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 or (resid 461 through 46 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 463 or (resi \ d 464 through 465 and (name N or name CA or name C or name O or name CB )) or re \ sid 466 through 473 or (resid 474 and (name N or name CA or name C or name O or \ name CB )) or resid 475 through 479 or (resid 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 or (resid 482 through 484 and (name N or \ name CA or name C or name O or name CB )) or resid 485 or (resid 486 through 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 or (resi \ d 489 through 502 and (name N or name CA or name C or name O or name CB )) or re \ sid 503 or (resid 504 through 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 526 or (resid 527 through 529 and (name N or nam \ e CA or name C or name O or name CB )) or resid 530 or (resid 531 through 539 an \ d (name N or name CA or name C or name O or name CB )) or resid 540 through 541 \ or (resid 542 and (name N or name CA or name C or name O or name CB )) or resid \ 543 through 544 or (resid 545 through 563 and (name N or name CA or name C or na \ me O or name CB )) or (resid 564 through 574 and (name N or name CA or name C or \ name O or name CB )) or (resid 575 through 591 and (name N or name CA or name C \ or name O or name CB )) or (resid 592 through 597 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 598 through 613 and (name N or name 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 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 92 or (resid 93 and (name N or name CA or name C or \ name O or name CB )) or resid 94 through 129 or (resid 130 and (name N or name \ CA or name C or name O or name CB )) or resid 131 through 180 or (resid 181 and \ (name N or name CA or name C or name O or name CB )) or resid 182 through 223 or \ (resid 224 through 226 and (name N or name CA or name C or name O or name CB )) \ or resid 227 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 (resid 251 and (name N or name CA o \ r name C or name O or name CB )) or resid 252 through 267 or (resid 268 and (nam \ e N or name CA or name C or name O or name CB )) or resid 269 through 273 or (re \ sid 274 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 through 356 or (resid 357 and (name N or name CA or name C or name O o \ r name CB )) or resid 358 through 415 or (resid 416 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or resid 420 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 through 42 or (resid 43 thro \ ugh 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thro \ ugh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 54 or (resid 55 and (name N or name CA or name C or name O or n \ ame CB )) or resid 56 through 85 or (resid 86 and (name N or name CA or name C o \ r name O or name CB )) or resid 87 through 92 or (resid 93 and (name N or name C \ A or name C or name O or name CB )) or resid 94 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 112 or (resid 113 through 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 139 or (resid 140 and (name N or \ name CA or name C or name O or name CB )) or resid 141 through 150 or (resid 15 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 163 or (resid 164 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C o \ r name O or name CB )) or resid 193 through 195 or (resid 196 and (name N or nam \ e CA or name C or name O or name CB )) or resid 197 through 205 or (resid 206 th \ rough 208 and (name N or name CA or name C or name O or name CB )) or resid 209 \ or (resid 210 and (name N or name CA or name C or name O or name CB )) or resid \ 211 through 225 or (resid 226 and (name N or name CA or name C or name O or name \ CB )) or resid 227 through 236 or (resid 237 through 238 and (name N or name CA \ or name C or name O or name CB )) or resid 239 through 242 or (resid 243 and (n \ ame N or name CA or name C or name O or name CB )) or resid 244 through 250 or ( \ resid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 \ through 256 or (resid 264 through 268 and (name N or name CA or name C or name O \ or name CB )) or resid 269 through 270 or (resid 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or (resid 284 through 286 and (na \ me N or name CA or name C or name O or name CB )) or resid 287 or (resid 288 thr \ ough 305 and (name N or name CA or name C or name O or name CB )) or (resid 306 \ through 311 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 2 or (resid 313 and (name N or name CA or name C or name O or name CB )) or resi \ d 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) or \ resid 316 through 319 or (resid 320 and (name N or name CA or name C or name O o \ r name CB )) or resid 321 through 329 or (resid 330 through 331 and (name N or n \ ame CA or name C or name O or name CB )) or resid 332 through 350 or (resid 351 \ and (name N or name CA or name C or name O or name CB )) or resid 352 through 35 \ 8 or (resid 359 and (name N or name CA or name C or name O or name CB )) or resi \ d 360 through 404 or (resid 405 and (name N or name CA or name C or name O or na \ me CB )) or resid 406 or (resid 407 and (name N or name CA or name C or name O o \ r name CB )) or resid 408 through 415 or (resid 416 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 420 through 425 and (name N o \ r name CA or name C or name O or name CB )) or resid 426 or (resid 427 through 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 440 or (resid 441 through 451 and (name N or name CA or name C or name O or nam \ e CB )) or resid 452 through 453 or (resid 454 through 459 and (name N or name C \ A or name C or name O or name CB )) or resid 460 through 461 or (resid 462 and ( \ name N or name CA or name C or name O or name CB )) or resid 463 or (resid 464 t \ hrough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 or (resid 482 through 484 and (name N or name CA or name C or n \ ame O or name CB )) or resid 485 or (resid 486 through 487 and (name N or name C \ A or name C or name O or name CB )) or resid 488 or (resid 489 through 502 and ( \ name N or name CA or name C or name O or name CB )) or (resid 503 through 521 an \ d (name N or name CA or name C or name O or name CB )) or resid 522 through 527 \ or (resid 528 through 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 or (resid 531 through 539 and (name N or name CA or name C or na \ me O or name CB )) or resid 540 through 541 or (resid 542 and (name N or name CA \ or name C or name O or name CB )) or resid 543 through 544 or (resid 545 throug \ h 563 and (name N or name CA or name C or name O or name CB )) or (resid 564 thr \ ough 574 and (name N or name CA or name C or name O or name CB )) or (resid 575 \ through 591 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 2 or (resid 593 through 597 and (name N or name CA or name C or name O or name C \ B )) or (resid 598 through 613 and (name N or name CA or name C or name O or nam \ e CB )))) } ncs_group { reference = (chain 'B' and ((resid 15 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 50 or (resid 51 through 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 60 or (re \ sid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 thro \ ugh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or \ resid 72 through 104 or (resid 105 through 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 115 or (resid 116 and (name N or na \ me CA or name C or name O or name CB )) or resid 117 through 128 or (resid 129 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 148 or (resid 149 and (name N or name CA or name C or name O or name CB \ )) or resid 150 through 161 or (resid 162 and (name N or name CA or name C or n \ ame O or name CB )) or resid 163 through 173 or (resid 174 through 176 and (name \ N or name CA or name C or name O or name CB )) or resid 177 through 180 or (res \ id 181 through 182 and (name N or name CA or name C or name O or name CB )) or r \ esid 183 through 194 or resid 207 through 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 name O or name CB )) or resid 219 through 220 or \ (resid 221 through 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 230 or (resid 231 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 throug \ h 238 or (resid 239 and (name N or name CA or name 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 250 or (resid 251 and (name N or n \ ame CA or name C or name O or name CB )) or resid 252 through 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 28 \ 1 or (resid 282 through 283 and (name N or name CA or name C or name O or name C \ B )) or resid 284 through 296 or (resid 297 and (name N or name CA or name C or \ name O or name CB )) or resid 298 through 300 or (resid 301 and (name N or name \ CA 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 31 \ 8 through 325 or (resid 326 and (name N or name CA or name C or name O or name C \ B )) or resid 327 through 335 or (resid 336 and (name N or name CA or name C or \ name O or name CB )) or resid 337 through 375 or (resid 376 and (name N or name \ CA or name C or name O or name CB )) or resid 377 or (resid 378 and (name N or n \ ame CA or name C or name O or name CB )) or resid 379 or (resid 380 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 name CB )) or (res \ id 388 through 392 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 and (name N or na \ me CA or name C or name O or name CB )) or resid 402 through 415 or (resid 416 t \ hrough 420 and (name N or name CA or name C or name O or name CB )) or (resid 42 \ 1 through 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 439 or (resid 440 through 441 and (name N or name CA or name C or na \ me O or name CB )) or resid 442 through 452 or (resid 453 and (name N or name CA \ or name C or name O or name CB )) or resid 454 through 458 or (resid 459 and (n \ ame 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 name C or name O or name CB )) o \ r 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 (name N or name CA or name C or na \ me O or name CB )) or resid 478 through 485)) selection = (chain 'D' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or nam \ e CA or name C or name O or name CB )) or resid 33 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 51 or (r \ esid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thr \ ough 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 83 or (resid 84 and (name N or name CA or name C or name O or \ name CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 128 or (resid 129 through 130 and (n \ ame N or name CA or name C or name O or name CB )) or resid 131 through 169 or ( \ resid 170 and (name N or name CA or name C or name O or name CB )) or resid 171 \ through 173 or (resid 174 through 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 through 220 or (resid 221 through 223 and (name N or \ name CA or name C or name O or name CB )) or resid 224 through 226 or (resid 22 \ 7 through 228 and (name N or name CA or name C or name O or name CB )) or resid \ 229 through 231 or (resid 232 and (name N or name CA or name C or name O or name \ CB )) or resid 233 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 289 or (resid 290 and (n \ ame N or name CA or name C or name O or name CB )) or resid 291 through 295 or ( \ resid 296 through 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 through 316 or (resid 317 and (name N or name CA or name C or name O \ or name CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or \ name C or name O or name CB )) or resid 337 through 384 or (resid 385 through 38 \ 7 and (name N or name CA or name C or name O or name 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 (r \ esid 394 through 395 and (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 na \ me C or name O or name CB )) or resid 431 or (resid 432 and (name N or name CA o \ r name C or name O or name CB )) or resid 433 through 439 or (resid 440 through \ 441 and (name N or name CA or name C or name O or name CB )) or resid 442 throug \ h 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 o \ r name CB )) or resid 484 through 485)) selection = (chain 'F' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or nam \ e CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and ( \ name N or name CA or name C or name O or name CB )) or resid 36 through 39 or (r \ esid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thr \ ough 50 or (resid 51 through 52 and (name N or name CA or name C or name O or na \ me CB )) or resid 53 through 58 or (resid 59 and (name N or name CA or name C or \ name O or name CB )) or resid 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 86 or (resid 87 and (na \ me N or name CA or name C or name O or name CB )) or resid 88 or (resid 89 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or r \ esid 95 through 98 or (resid 99 and (name N or name CA or name C or name O or na \ me CB )) or resid 100 through 104 or (resid 105 through 107 and (name N or name \ CA or name C or name O or name CB )) or resid 108 through 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )) or resid 119 through 169 or \ (resid 170 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 1 through 180 or (resid 181 through 182 and (name N or name CA or name C or name \ O or name CB )) or resid 183 through 208 or (resid 209 and (name N or name CA o \ r name C or name O or name CB )) or resid 210 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 222 or (re \ sid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 227 or (resid 228 and (name N or name CA or name C or name O or name CB )) \ or resid 229 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name CA o \ r name C or name O or name CB )) or resid 240 through 281 or (resid 282 through \ 283 and (name N or name CA or name C or name O or name CB )) or resid 284 throug \ h 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 327 or (resid 328 and (name N or name CA or name C or name O o \ r name CB )) or resid 329 through 338 or (resid 339 through 341 and (name N or n \ ame CA or name C or name O or name CB )) or resid 342 through 375 or (resid 376 \ and (name N or name CA or name C or name O or name CB )) or resid 377 through 37 \ 9 or (resid 380 and (name N or name CA or name C or name O or name CB )) or resi \ d 381 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 name CA or name C \ or name O or name CB )) or resid 393 through 394 or (resid 395 and (name N or na \ me CA or name C or name O or name CB )) or resid 396 through 397 or (resid 398 a \ nd (name N or name CA or name C or name O or name CB )) or resid 399 or (resid 4 \ 00 through 401 and (name N or name CA or name C or name O or name CB )) or resid \ 402 through 431 or (resid 432 and (name N or name CA or name C or name O or nam \ e CB )) or resid 433 through 452 or (resid 453 and (name N or name CA or name C \ or name O or name CB )) or resid 454 through 455 or (resid 456 and (name N or na \ me CA or name C or name O or name CB )) or resid 457 through 458 or (resid 459 a \ nd (name N or name CA or name C or name O or name CB )) or resid 460 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 476 or (resid 477 and (name N or name CA or name C or name O or nam \ e CB )) or resid 478 through 485)) } ncs_group { reference = (chain 'G' and ((resid 32 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 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 94 or (resid 95 and (n \ ame N or name CA or name C or name O or name CB )) or resid 96 through 101 or (r \ esid 102 through 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 133 or (resid 134 and (name N or \ name CA or name C or name O or name CB )) or resid 135 or (resid 136 through 137 \ and (name N or name CA or name C or name O or name CB )) or resid 138 through 1 \ 41 or (resid 142 through 143 and (name N or name CA or name C or name O or name \ CB )) or resid 144 through 145 or (resid 146 through 148 and (name N or name CA \ or name C or name O or name CB )) or resid 149 through 157 or (resid 158 through \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 throu \ gh 174 or (resid 175 through 178 and (name N or name CA or name C or name O or n \ ame CB )) or resid 179 through 183 or (resid 184 through 185 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 204 o \ r (resid 205 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 06 through 229 or (resid 230 through 231 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'I' and (resid 32 through 102 or (resid 103 through 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 122 or (resid 123 a \ nd (name N or name CA or name C or name O or name CB )) or resid 124 through 157 \ or (resid 158 through 159 and (name N or name CA or name C or name O or name CB \ )) or resid 160 through 165 or (resid 166 through 167 and (name N or name CA or \ name C or name O or name CB )) or resid 168 through 183 or (resid 184 through 1 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 186 through \ 191 or (resid 192 through 196 and (name N or name CA or name C or name O or nam \ e CB )) or resid 197 or (resid 198 and (name N or name CA or name C or name O or \ name CB )) or resid 199 or (resid 200 and (name N or name CA or name C or name \ O or name CB )) or resid 201 through 210 or (resid 211 through 214 and (name N o \ r name CA or name C or name O or name CB )) or resid 215 through 220 or (resid 2 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 231)) selection = (chain 'K' and ((resid 32 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 name CA or name C or name \ O or name CB )) or resid 88 through 103 or (resid 104 through 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 109 or (resid 11 \ 0 through 116 and (name N or name CA or name C or name O or name CB )) or resid \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or re \ sid 119 through 135 or (resid 136 through 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 139 or (resid 140 through 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 or (resid 145 th \ rough 148 and (name N or name CA or name C or name O or name CB )) or resid 149 \ through 154 or (resid 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 through 158 or (resid 159 and (name N or name CA or name C or na \ me O or name CB )) or resid 160 through 175 or (resid 176 through 178 and (name \ N or name CA or name C or name O or name CB )) or resid 179 through 191 or (resi \ d 192 through 196 and (name N or name CA or name C or name O or name CB )) or re \ sid 197 through 230 or (resid 231 and (name N or name CA or name C or name O or \ name CB )))) } ncs_group { reference = (chain 'H' and ((resid 32 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 and (name N or name CA or name C or name \ O or name CB )) or resid 80 through 112)) selection = (chain 'L' and (resid 32 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 a \ nd (name N or name CA or name C or name O or name CB )) or resid 110 through 112 \ )) } 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 5 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 20130 2.51 5 N 5698 2.21 5 O 5642 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: 3.060 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: 0.020 Extract box with map and model: 15.780 Check model and map are aligned: 0.490 Process input model: 81.930 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 32067 Z= 0.197 Angle : 0.509 9.998 44004 Z= 0.279 Chirality : 0.041 0.226 5489 Planarity : 0.004 0.069 5734 Dihedral : 12.332 142.713 9988 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.41 (0.13), residues: 4774 helix: 2.48 (0.11), residues: 2399 sheet: -1.61 (0.24), residues: 474 loop : -0.38 (0.15), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 442 time to evaluate : 3.717 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 444 average time/residue: 0.4754 time to fit residues: 331.8430 Evaluate side-chains 354 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2561 time to fit residues: 5.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 372 optimal weight: 50.0000 chunk 144 optimal weight: 40.0000 chunk 226 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 431 optimal weight: 50.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.081 32067 Z= 0.498 Angle : 0.598 11.851 44004 Z= 0.312 Chirality : 0.045 0.195 5489 Planarity : 0.005 0.071 5734 Dihedral : 4.963 117.404 5112 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 4774 helix: 2.22 (0.11), residues: 2381 sheet: -1.95 (0.22), residues: 518 loop : -0.54 (0.15), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 353 time to evaluate : 3.811 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 374 average time/residue: 0.4560 time to fit residues: 273.4340 Evaluate side-chains 363 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 334 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2782 time to fit residues: 20.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 239 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 359 optimal weight: 0.5980 chunk 293 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 432 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 384 optimal weight: 2.9990 chunk 428 optimal weight: 50.0000 chunk 147 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 243 ASN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 32067 Z= 0.395 Angle : 0.545 11.072 44004 Z= 0.281 Chirality : 0.043 0.218 5489 Planarity : 0.004 0.067 5734 Dihedral : 4.887 119.462 5112 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 4774 helix: 2.19 (0.11), residues: 2379 sheet: -1.99 (0.22), residues: 502 loop : -0.57 (0.15), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 363 time to evaluate : 3.640 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 387 average time/residue: 0.4486 time to fit residues: 279.7668 Evaluate side-chains 358 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 339 time to evaluate : 4.013 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3274 time to fit residues: 16.5292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 426 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 206 optimal weight: 0.5980 chunk 290 optimal weight: 0.5980 chunk 433 optimal weight: 7.9990 chunk 459 optimal weight: 40.0000 chunk 226 optimal weight: 0.7980 chunk 411 optimal weight: 40.0000 chunk 123 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 32067 Z= 0.278 Angle : 0.496 9.857 44004 Z= 0.256 Chirality : 0.042 0.168 5489 Planarity : 0.004 0.062 5734 Dihedral : 4.751 116.617 5112 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.13), residues: 4774 helix: 2.25 (0.11), residues: 2388 sheet: -1.96 (0.22), residues: 511 loop : -0.51 (0.15), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 370 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 394 average time/residue: 0.4810 time to fit residues: 303.8545 Evaluate side-chains 371 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 350 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2965 time to fit residues: 17.2502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 382 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 341 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 391 optimal weight: 30.0000 chunk 317 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 115 optimal weight: 0.0470 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 32067 Z= 0.397 Angle : 0.546 14.739 44004 Z= 0.280 Chirality : 0.043 0.198 5489 Planarity : 0.004 0.062 5734 Dihedral : 4.845 114.939 5112 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 4774 helix: 2.20 (0.11), residues: 2387 sheet: -2.02 (0.22), residues: 522 loop : -0.56 (0.15), residues: 1865 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 348 time to evaluate : 4.008 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 382 average time/residue: 0.4645 time to fit residues: 285.3625 Evaluate side-chains 362 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 338 time to evaluate : 3.981 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2821 time to fit residues: 18.2411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 154 optimal weight: 5.9990 chunk 413 optimal weight: 30.0000 chunk 90 optimal weight: 0.4980 chunk 269 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 459 optimal weight: 30.0000 chunk 381 optimal weight: 0.5980 chunk 212 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 152 optimal weight: 50.0000 chunk 241 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32067 Z= 0.194 Angle : 0.473 12.936 44004 Z= 0.243 Chirality : 0.041 0.250 5489 Planarity : 0.003 0.058 5734 Dihedral : 4.619 115.237 5112 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 4774 helix: 2.38 (0.11), residues: 2389 sheet: -1.97 (0.22), residues: 532 loop : -0.41 (0.15), residues: 1853 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 389 time to evaluate : 3.828 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 413 average time/residue: 0.4638 time to fit residues: 309.0898 Evaluate side-chains 372 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 355 time to evaluate : 4.044 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3492 time to fit residues: 15.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 443 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 335 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 386 optimal weight: 5.9990 chunk 256 optimal weight: 0.5980 chunk 457 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 32067 Z= 0.406 Angle : 0.557 15.627 44004 Z= 0.284 Chirality : 0.044 0.242 5489 Planarity : 0.004 0.057 5734 Dihedral : 4.791 116.448 5112 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4774 helix: 2.25 (0.11), residues: 2386 sheet: -1.99 (0.22), residues: 546 loop : -0.50 (0.15), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 348 time to evaluate : 3.820 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 364 average time/residue: 0.4949 time to fit residues: 289.0572 Evaluate side-chains 352 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 337 time to evaluate : 3.488 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2924 time to fit residues: 13.5865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 283 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 291 optimal weight: 1.9990 chunk 311 optimal weight: 0.0370 chunk 226 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 359 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 32067 Z= 0.192 Angle : 0.475 13.594 44004 Z= 0.242 Chirality : 0.041 0.185 5489 Planarity : 0.003 0.054 5734 Dihedral : 4.574 116.097 5112 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 4774 helix: 2.41 (0.11), residues: 2384 sheet: -1.86 (0.22), residues: 557 loop : -0.39 (0.15), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 372 time to evaluate : 3.973 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 384 average time/residue: 0.4820 time to fit residues: 297.4478 Evaluate side-chains 369 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 360 time to evaluate : 3.665 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2934 time to fit residues: 9.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 416 optimal weight: 2.9990 chunk 438 optimal weight: 20.0000 chunk 400 optimal weight: 0.5980 chunk 426 optimal weight: 50.0000 chunk 256 optimal weight: 0.0070 chunk 185 optimal weight: 0.9990 chunk 335 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 385 optimal weight: 0.8980 chunk 403 optimal weight: 3.9990 chunk 425 optimal weight: 30.0000 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 32067 Z= 0.207 Angle : 0.482 13.782 44004 Z= 0.244 Chirality : 0.041 0.169 5489 Planarity : 0.004 0.052 5734 Dihedral : 4.527 115.030 5112 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.31 (0.13), residues: 4774 helix: 2.44 (0.11), residues: 2393 sheet: -1.80 (0.21), residues: 568 loop : -0.34 (0.15), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 377 time to evaluate : 3.996 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 383 average time/residue: 0.4728 time to fit residues: 290.2635 Evaluate side-chains 361 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 3.638 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2838 time to fit residues: 7.0718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 280 optimal weight: 1.9990 chunk 451 optimal weight: 40.0000 chunk 275 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 313 optimal weight: 40.0000 chunk 473 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 32067 Z= 0.400 Angle : 0.565 16.151 44004 Z= 0.285 Chirality : 0.043 0.213 5489 Planarity : 0.004 0.053 5734 Dihedral : 4.759 116.566 5112 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.12 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.13 (0.13), residues: 4774 helix: 2.27 (0.11), residues: 2394 sheet: -1.87 (0.22), residues: 525 loop : -0.45 (0.15), residues: 1855 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 350 time to evaluate : 3.861 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 359 average time/residue: 0.5068 time to fit residues: 288.1345 Evaluate side-chains 356 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 346 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3015 time to fit residues: 11.4814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 299 optimal weight: 1.9990 chunk 401 optimal weight: 0.5980 chunk 115 optimal weight: 0.0060 chunk 347 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 377 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 387 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.0050 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN E 491 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121067 restraints weight = 41431.871| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.36 r_work: 0.3216 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 32067 Z= 0.168 Angle : 0.476 15.233 44004 Z= 0.241 Chirality : 0.041 0.155 5489 Planarity : 0.003 0.052 5734 Dihedral : 4.527 115.588 5112 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.32 (0.13), residues: 4774 helix: 2.45 (0.11), residues: 2392 sheet: -1.85 (0.21), residues: 560 loop : -0.33 (0.15), residues: 1822 =============================================================================== Job complete usr+sys time: 6904.43 seconds wall clock time: 126 minutes 8.09 seconds (7568.09 seconds total)