Starting phenix.real_space_refine on Fri Jul 26 03:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rsc_19476/07_2024/8rsc_19476.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 138 5.16 5 C 19758 2.51 5 N 5773 2.21 5 O 6185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 738": "OE1" <-> "OE2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E GLU 607": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F GLU 737": "OE1" <-> "OE2" Residue "F GLU 738": "OE1" <-> "OE2" Time to flip residues: 0.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31874 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 5262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5262 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 315 Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 303 Chain: "D" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5263 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 307 Chain: "E" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5260 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 310 Chain: "F" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 303 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.34, per 1000 atoms: 0.51 Number of scatterers: 31874 At special positions: 0 Unit cell: (169.42, 174.58, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 20 15.00 O 6185 8.00 N 5773 7.00 C 19758 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: 11.57 Conformation dependent library (CDL) restraints added in 5.8 seconds 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8338 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 34 sheets defined 50.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.668A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 Processing helix chain 'A' and resid 203 through 206 removed outlier: 4.064A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.556A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.938A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 295 removed outlier: 3.727A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 333 removed outlier: 4.082A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.643A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.744A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 3.695A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.930A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.731A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.094A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.623A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 4.055A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.632A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 4.267A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.835A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.595A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 716 removed outlier: 3.902A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.591A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.658A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.689A pdb=" N ASP B 205 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.910A pdb=" N LEU B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.841A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 295 removed outlier: 4.091A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.566A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.551A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.648A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.521A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.802A pdb=" N GLU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 434' Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.951A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.737A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.659A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.612A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 4.077A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.682A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.297A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.536A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.552A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 removed outlier: 4.380A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.644A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.537A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.756A pdb=" N MET C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 47' Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.117A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.838A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.632A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.074A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.594A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.877A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.680A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 432 removed outlier: 3.760A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.980A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.037A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.200A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.691A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.530A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.340A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.885A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.586A pdb=" N LYS C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.679A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.693A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 716 removed outlier: 3.604A pdb=" N LEU C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.677A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 3.762A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.856A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 removed outlier: 4.181A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.165A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.989A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 318 through 338 removed outlier: 3.523A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.888A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 4.003A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 432 removed outlier: 4.496A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.960A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.952A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.146A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.523A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 removed outlier: 3.582A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.368A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.758A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 615 removed outlier: 3.649A pdb=" N LYS D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 612 through 615' Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.543A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.614A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.525A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.662A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR D 715 " --> pdb=" O ARG D 711 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.769A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.864A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.619A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 140 removed outlier: 3.765A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.516A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 removed outlier: 4.007A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.717A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 336 removed outlier: 3.643A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.814A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 4.072A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 435 removed outlier: 5.725A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.955A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.913A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.293A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 4.025A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 554 removed outlier: 3.530A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.849A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.756A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 removed outlier: 3.776A pdb=" N LYS E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 612 through 615' Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.940A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.627A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 716 removed outlier: 3.637A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR E 715 " --> pdb=" O ARG E 711 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.754A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 removed outlier: 3.866A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 140 removed outlier: 4.330A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 removed outlier: 4.123A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.710A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 336 removed outlier: 3.513A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.795A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.820A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 430 removed outlier: 3.656A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.241A pdb=" N ASP F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 430 through 435' Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.819A pdb=" N LEU F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.530A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.505A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.030A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.939A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 removed outlier: 3.515A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.409A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 4.081A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 615 removed outlier: 3.640A pdb=" N LYS F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.618A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.615A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.661A pdb=" N LEU F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 715 " --> pdb=" O ARG F 711 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.725A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 removed outlier: 3.747A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.665A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.342A pdb=" N LEU B 117 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.504A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.731A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.442A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.788A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 70 Processing sheet with id=AB8, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.450A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.767A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 70 Processing sheet with id=AC5, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC6, first strand: chain 'E' and resid 116 through 118 Processing sheet with id=AC7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.518A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.816A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'F' and resid 41 through 42 removed outlier: 5.381A pdb=" N LEU F 41 " --> pdb=" O ASP F 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 65 through 69 Processing sheet with id=AD3, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'F' and resid 116 through 117 Processing sheet with id=AD5, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AD6, first strand: chain 'F' and resid 265 through 270 removed outlier: 3.737A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.809A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3867 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: 11.24 Time building geometry restraints manager: 12.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6184 1.32 - 1.45: 6967 1.45 - 1.57: 18904 1.57 - 1.69: 31 1.69 - 1.81: 234 Bond restraints: 32320 Sorted by residual: bond pdb=" CA ARG A 191 " pdb=" C ARG A 191 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.12e-02 7.97e+03 1.49e+01 bond pdb=" CA GLU B 200 " pdb=" C GLU B 200 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.10e-02 8.26e+03 1.11e+01 bond pdb=" CG GLU A 402 " pdb=" CD GLU A 402 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.00e+01 bond pdb=" N ARG A 191 " pdb=" CA ARG A 191 " ideal model delta sigma weight residual 1.462 1.433 0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N VAL B 201 " pdb=" CA VAL B 201 " ideal model delta sigma weight residual 1.461 1.434 0.027 1.17e-02 7.31e+03 5.48e+00 ... (remaining 32315 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.41: 940 106.41 - 113.85: 18275 113.85 - 121.28: 15842 121.28 - 128.71: 8728 128.71 - 136.14: 140 Bond angle restraints: 43925 Sorted by residual: angle pdb=" C ALA D 339 " pdb=" N HIS D 340 " pdb=" CA HIS D 340 " ideal model delta sigma weight residual 122.34 135.39 -13.05 1.39e+00 5.18e-01 8.81e+01 angle pdb=" C PRO B 223 " pdb=" N LEU B 224 " pdb=" CA LEU B 224 " ideal model delta sigma weight residual 120.44 132.16 -11.72 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N GLU A 192 " pdb=" CA GLU A 192 " pdb=" C GLU A 192 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.48e+01 angle pdb=" C ARG E 638 " pdb=" N LEU E 639 " pdb=" CA LEU E 639 " ideal model delta sigma weight residual 122.16 134.12 -11.96 1.50e+00 4.44e-01 6.35e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 110.42 116.56 -6.14 9.60e-01 1.09e+00 4.09e+01 ... (remaining 43920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 18223 22.01 - 44.02: 1367 44.02 - 66.02: 185 66.02 - 88.03: 48 88.03 - 110.04: 8 Dihedral angle restraints: 19831 sinusoidal: 7006 harmonic: 12825 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 -170.04 110.04 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ARG A 144 " pdb=" C ARG A 144 " pdb=" N PRO A 145 " pdb=" CA PRO A 145 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE E 423 " pdb=" C ILE E 423 " pdb=" N ARG E 424 " pdb=" CA ARG E 424 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 19828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4284 0.055 - 0.111: 686 0.111 - 0.166: 130 0.166 - 0.221: 4 0.221 - 0.277: 3 Chirality restraints: 5107 Sorted by residual: chirality pdb=" CA GLU A 194 " pdb=" N GLU A 194 " pdb=" C GLU A 194 " pdb=" CB GLU A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA VAL F 201 " pdb=" N VAL F 201 " pdb=" C VAL F 201 " pdb=" CB VAL F 201 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5104 not shown) Planarity restraints: 5890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 222 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO B 223 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 635 " 0.050 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO E 636 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 636 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 636 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 398 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C GLN A 398 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN A 398 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 399 " 0.017 2.00e-02 2.50e+03 ... (remaining 5887 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 308 2.58 - 3.16: 27662 3.16 - 3.74: 46395 3.74 - 4.32: 59953 4.32 - 4.90: 100966 Nonbonded interactions: 235284 Sorted by model distance: nonbonded pdb=" OH TYR D 244 " pdb=" OE1 GLN D 568 " model vdw 1.995 2.440 nonbonded pdb=" O GLU A 440 " pdb=" OG SER A 444 " model vdw 2.010 2.440 nonbonded pdb=" OG1 THR B 448 " pdb=" OD1 ASP B 450 " model vdw 2.089 2.440 nonbonded pdb=" O ALA C 455 " pdb=" OG SER C 459 " model vdw 2.099 2.440 nonbonded pdb=" NH1 ARG A 377 " pdb=" O THR A 403 " model vdw 2.118 2.520 ... (remaining 235279 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 21 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name N o \ r name CA or name C or name O or name CB )) or resid 761 through 762 or resid 90 \ 1)) selection = (chain 'B' and (resid 21 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 762 or resid 901)) selection = (chain 'C' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) selection = (chain 'D' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) selection = (chain 'E' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 759 or (resid 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 through 762 or resid 902)) selection = (chain 'F' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 78.670 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 0.084 32320 Z= 0.204 Angle : 0.643 13.047 43925 Z= 0.360 Chirality : 0.042 0.277 5107 Planarity : 0.004 0.074 5890 Dihedral : 15.625 110.038 11493 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.04 % Favored : 92.94 % Rotamer: Outliers : 0.11 % Allowed : 15.96 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % 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: -1.45 (0.13), residues: 4445 helix: 0.38 (0.13), residues: 1779 sheet: -0.57 (0.22), residues: 586 loop : -2.34 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS A 499 PHE 0.010 0.001 PHE E 674 TYR 0.011 0.001 TYR B 244 ARG 0.003 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 354 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 734 ASP cc_start: 0.5873 (p0) cc_final: 0.4770 (t70) REVERT: C 403 THR cc_start: 0.8098 (m) cc_final: 0.7878 (m) REVERT: C 465 ARG cc_start: 0.6745 (mmp80) cc_final: 0.6527 (ptm-80) REVERT: D 465 ARG cc_start: 0.6452 (mmp80) cc_final: 0.6074 (ttm170) REVERT: D 745 ARG cc_start: 0.6101 (mtp-110) cc_final: 0.5712 (mtt180) outliers start: 3 outliers final: 3 residues processed: 357 average time/residue: 0.4397 time to fit residues: 246.9056 Evaluate side-chains 327 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain F residue 568 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 227 optimal weight: 50.0000 chunk 179 optimal weight: 0.9990 chunk 348 optimal weight: 0.0980 chunk 134 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 406 HIS ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 317 HIS C 340 HIS C 660 ASN C 714 GLN D 215 GLN D 382 GLN D 616 ASN D 714 GLN E 602 ASN F 404 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32320 Z= 0.189 Angle : 0.606 10.828 43925 Z= 0.302 Chirality : 0.045 0.171 5107 Planarity : 0.004 0.061 5890 Dihedral : 6.119 95.082 4843 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 2.39 % Allowed : 15.17 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4445 helix: 0.67 (0.13), residues: 1833 sheet: -0.41 (0.22), residues: 579 loop : -1.93 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 476 HIS 0.004 0.001 HIS C 340 PHE 0.014 0.001 PHE C 575 TYR 0.029 0.002 TYR B 203 ARG 0.004 0.000 ARG F 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 357 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 639 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7887 (mt) REVERT: C 465 ARG cc_start: 0.6748 (mmp80) cc_final: 0.6506 (ptm-80) REVERT: C 720 MET cc_start: 0.2982 (tpt) cc_final: 0.2596 (tpt) REVERT: D 449 MET cc_start: 0.6973 (tpt) cc_final: 0.6537 (tpt) REVERT: D 465 ARG cc_start: 0.6360 (mmp80) cc_final: 0.6064 (ttm170) REVERT: D 508 MET cc_start: 0.3998 (tpt) cc_final: 0.3562 (tpt) REVERT: D 625 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7893 (mtp85) REVERT: D 722 VAL cc_start: -0.2673 (OUTLIER) cc_final: -0.2914 (t) REVERT: D 731 ILE cc_start: 0.5970 (mp) cc_final: 0.5710 (pt) REVERT: D 745 ARG cc_start: 0.6127 (mtp-110) cc_final: 0.5697 (mtt180) REVERT: F 450 ASP cc_start: 0.6568 (m-30) cc_final: 0.6346 (m-30) REVERT: F 542 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8299 (mp) REVERT: F 598 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7482 (p0) outliers start: 67 outliers final: 31 residues processed: 403 average time/residue: 0.4274 time to fit residues: 275.8493 Evaluate side-chains 343 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 568 GLN Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 403 optimal weight: 2.9990 chunk 436 optimal weight: 0.8980 chunk 359 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 340 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 260 ASN B 296 ASN B 499 HIS B 660 ASN C 340 HIS C 490 GLN D 382 GLN D 602 ASN D 692 GLN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32320 Z= 0.197 Angle : 0.585 7.739 43925 Z= 0.289 Chirality : 0.045 0.164 5107 Planarity : 0.004 0.064 5890 Dihedral : 5.751 90.624 4840 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.53 % Allowed : 15.78 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.65 (0.13), residues: 4445 helix: 0.81 (0.13), residues: 1855 sheet: -0.35 (0.21), residues: 617 loop : -1.68 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 476 HIS 0.005 0.001 HIS F 406 PHE 0.034 0.001 PHE E 674 TYR 0.023 0.002 TYR F 244 ARG 0.006 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 362 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 508 MET cc_start: 0.6648 (tpp) cc_final: 0.6215 (tpp) REVERT: A 678 MET cc_start: 0.6906 (mmm) cc_final: 0.5788 (ttm) REVERT: B 486 LYS cc_start: 0.6950 (mttt) cc_final: 0.6693 (ttpp) REVERT: B 639 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 445 LEU cc_start: 0.6728 (tp) cc_final: 0.6490 (mt) REVERT: C 465 ARG cc_start: 0.6807 (mmp80) cc_final: 0.6463 (ptm-80) REVERT: C 534 GLU cc_start: 0.6487 (tm-30) cc_final: 0.6155 (tm-30) REVERT: C 720 MET cc_start: 0.3317 (tpt) cc_final: 0.2918 (tpt) REVERT: C 744 ARG cc_start: 0.4945 (ptm160) cc_final: 0.4016 (ptp-170) REVERT: D 424 ARG cc_start: 0.5333 (OUTLIER) cc_final: 0.4756 (ptp-110) REVERT: D 449 MET cc_start: 0.7002 (tpt) cc_final: 0.6766 (tpt) REVERT: D 464 LEU cc_start: 0.7702 (tm) cc_final: 0.6965 (tm) REVERT: D 465 ARG cc_start: 0.6478 (mmp80) cc_final: 0.6020 (ttm170) REVERT: D 625 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7971 (mtp85) REVERT: D 722 VAL cc_start: -0.2564 (OUTLIER) cc_final: -0.2770 (t) REVERT: D 732 ARG cc_start: 0.6967 (ptt-90) cc_final: 0.6537 (ptt180) REVERT: E 460 ASN cc_start: 0.6136 (t0) cc_final: 0.5841 (t0) REVERT: E 577 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7761 (p0) REVERT: E 751 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: F 450 ASP cc_start: 0.6685 (m-30) cc_final: 0.6436 (m-30) REVERT: F 542 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8332 (mp) REVERT: F 657 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7158 (mm) outliers start: 99 outliers final: 57 residues processed: 430 average time/residue: 0.4352 time to fit residues: 295.9390 Evaluate side-chains 377 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 312 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 9.9990 chunk 303 optimal weight: 50.0000 chunk 209 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 384 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN B 348 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 340 HIS C 490 GLN D 285 ASN D 660 ASN E 285 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32320 Z= 0.286 Angle : 0.653 7.165 43925 Z= 0.326 Chirality : 0.047 0.218 5107 Planarity : 0.005 0.070 5890 Dihedral : 5.873 90.735 4837 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.71 % Allowed : 16.71 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.75 (0.13), residues: 4445 helix: 0.69 (0.12), residues: 1835 sheet: -0.22 (0.21), residues: 582 loop : -1.72 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 476 HIS 0.008 0.001 HIS F 735 PHE 0.016 0.002 PHE E 265 TYR 0.014 0.002 TYR B 244 ARG 0.007 0.001 ARG E 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 349 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8545 (mt) REVERT: A 508 MET cc_start: 0.6721 (tpp) cc_final: 0.6190 (tpp) REVERT: B 486 LYS cc_start: 0.7025 (mttt) cc_final: 0.6753 (ttpp) REVERT: B 598 ASP cc_start: 0.7754 (p0) cc_final: 0.7525 (p0) REVERT: B 639 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8128 (mt) REVERT: B 680 ASN cc_start: 0.6960 (t0) cc_final: 0.5689 (p0) REVERT: C 465 ARG cc_start: 0.6895 (mmp80) cc_final: 0.6404 (ptm-80) REVERT: C 534 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6232 (tm-30) REVERT: C 568 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6864 (mt0) REVERT: C 720 MET cc_start: 0.3475 (tpt) cc_final: 0.3096 (tpt) REVERT: C 723 GLU cc_start: 0.0233 (OUTLIER) cc_final: -0.0252 (tt0) REVERT: D 389 LYS cc_start: 0.7398 (tptp) cc_final: 0.6710 (mtmt) REVERT: D 449 MET cc_start: 0.7138 (tpt) cc_final: 0.6926 (tpt) REVERT: D 464 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7075 (tm) REVERT: D 465 ARG cc_start: 0.6846 (mmp80) cc_final: 0.6112 (ttm170) REVERT: D 560 ARG cc_start: 0.7203 (ttm170) cc_final: 0.7001 (mtm180) REVERT: D 625 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7873 (mtp85) REVERT: D 677 LYS cc_start: 0.6342 (pttt) cc_final: 0.6015 (mtmt) REVERT: D 722 VAL cc_start: -0.2500 (OUTLIER) cc_final: -0.2718 (t) REVERT: E 402 GLU cc_start: 0.7004 (pt0) cc_final: 0.6604 (pt0) REVERT: E 460 ASN cc_start: 0.6219 (t0) cc_final: 0.5840 (t0) REVERT: E 577 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (p0) REVERT: E 599 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7709 (mtp180) REVERT: E 666 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7736 (p) REVERT: E 751 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: F 252 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8379 (m) REVERT: F 542 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8410 (mp) outliers start: 132 outliers final: 84 residues processed: 449 average time/residue: 0.4519 time to fit residues: 324.6001 Evaluate side-chains 409 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 313 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 319 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 366 optimal weight: 0.0270 chunk 296 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 chunk 385 optimal weight: 40.0000 chunk 108 optimal weight: 4.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32320 Z= 0.283 Angle : 0.630 9.105 43925 Z= 0.313 Chirality : 0.046 0.171 5107 Planarity : 0.005 0.069 5890 Dihedral : 5.832 92.061 4837 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.64 % Allowed : 18.21 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.75 (0.13), residues: 4445 helix: 0.67 (0.12), residues: 1837 sheet: -0.20 (0.22), residues: 561 loop : -1.70 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 476 HIS 0.008 0.001 HIS F 735 PHE 0.037 0.002 PHE E 674 TYR 0.016 0.002 TYR D 244 ARG 0.013 0.001 ARG C 753 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 341 time to evaluate : 3.442 Fit side-chains revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8504 (mt) REVERT: A 508 MET cc_start: 0.6418 (tpp) cc_final: 0.6012 (tpp) REVERT: A 661 LEU cc_start: 0.7506 (mt) cc_final: 0.7010 (mp) REVERT: A 678 MET cc_start: 0.7313 (mmm) cc_final: 0.6198 (ttm) REVERT: B 390 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7559 (mt) REVERT: B 639 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8172 (mt) REVERT: C 426 LYS cc_start: 0.6544 (mmmm) cc_final: 0.6241 (mtmt) REVERT: C 445 LEU cc_start: 0.7009 (tp) cc_final: 0.6674 (mt) REVERT: C 465 ARG cc_start: 0.7026 (mmp80) cc_final: 0.6388 (ptm-80) REVERT: C 534 GLU cc_start: 0.6581 (tm-30) cc_final: 0.6246 (tm-30) REVERT: C 568 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6843 (mt0) REVERT: C 720 MET cc_start: 0.3618 (tpt) cc_final: 0.3183 (tpt) REVERT: D 336 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6716 (mmtm) REVERT: D 449 MET cc_start: 0.7179 (tpt) cc_final: 0.6934 (tpt) REVERT: D 464 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7094 (tm) REVERT: D 465 ARG cc_start: 0.6910 (mmp80) cc_final: 0.6135 (ttm170) REVERT: D 560 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7045 (mtm-85) REVERT: D 625 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7933 (mtp85) REVERT: E 337 GLN cc_start: 0.6749 (mm110) cc_final: 0.6191 (pp30) REVERT: E 515 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8759 (tt) REVERT: E 577 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7887 (p0) REVERT: E 599 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7659 (mtp180) REVERT: E 666 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7745 (p) REVERT: E 751 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6419 (m-30) REVERT: F 252 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8351 (m) REVERT: F 283 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: F 542 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8411 (mp) REVERT: F 657 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7261 (mm) outliers start: 130 outliers final: 83 residues processed: 438 average time/residue: 0.4156 time to fit residues: 291.8327 Evaluate side-chains 417 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 320 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 429 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 225 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 494 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 536 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32320 Z= 0.333 Angle : 0.674 8.042 43925 Z= 0.337 Chirality : 0.048 0.188 5107 Planarity : 0.005 0.076 5890 Dihedral : 6.029 92.276 4837 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.50 % Allowed : 18.24 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 4445 helix: 0.48 (0.12), residues: 1841 sheet: -0.33 (0.21), residues: 560 loop : -1.79 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 476 HIS 0.008 0.001 HIS F 735 PHE 0.018 0.002 PHE F 674 TYR 0.019 0.002 TYR D 244 ARG 0.012 0.001 ARG C 753 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 333 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.7137 (mmm) cc_final: 0.6303 (ttm) REVERT: A 763 GLN cc_start: 0.2446 (OUTLIER) cc_final: 0.1672 (pt0) REVERT: B 390 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7543 (mt) REVERT: B 639 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8245 (mt) REVERT: C 338 ARG cc_start: 0.6740 (ptt-90) cc_final: 0.6536 (ptp-170) REVERT: C 424 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6052 (ptt-90) REVERT: C 426 LYS cc_start: 0.6677 (mmmm) cc_final: 0.6429 (mtmt) REVERT: C 465 ARG cc_start: 0.7108 (mmp80) cc_final: 0.6661 (ptp-170) REVERT: C 473 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7076 (mm110) REVERT: C 534 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6301 (tm-30) REVERT: C 568 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: C 661 LEU cc_start: 0.7299 (mm) cc_final: 0.7002 (mt) REVERT: C 720 MET cc_start: 0.3793 (tpt) cc_final: 0.3381 (tpt) REVERT: C 723 GLU cc_start: 0.0726 (OUTLIER) cc_final: 0.0240 (tt0) REVERT: C 744 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5610 (ttm170) REVERT: D 283 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: D 336 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6739 (mmtm) REVERT: D 389 LYS cc_start: 0.7319 (tptp) cc_final: 0.6844 (mtmt) REVERT: D 449 MET cc_start: 0.7181 (tpt) cc_final: 0.6946 (tpt) REVERT: D 465 ARG cc_start: 0.7105 (mmp80) cc_final: 0.6156 (ttm170) REVERT: E 402 GLU cc_start: 0.7065 (pt0) cc_final: 0.6682 (pt0) REVERT: E 515 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8776 (tt) REVERT: E 577 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7949 (p0) REVERT: E 599 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7778 (mtp180) REVERT: E 666 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7744 (p) REVERT: E 683 SER cc_start: 0.7253 (p) cc_final: 0.6926 (m) REVERT: E 714 GLN cc_start: 0.2913 (OUTLIER) cc_final: 0.2610 (tp40) REVERT: F 252 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8382 (m) REVERT: F 283 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6552 (mt-10) REVERT: F 479 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7488 (mm) REVERT: F 542 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8432 (mp) REVERT: F 657 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7323 (mm) outliers start: 154 outliers final: 98 residues processed: 450 average time/residue: 0.4323 time to fit residues: 313.1497 Evaluate side-chains 434 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 318 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 313 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 361 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 8.9990 chunk 267 optimal weight: 0.0010 chunk 260 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 overall best weight: 3.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN C 340 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32320 Z= 0.297 Angle : 0.640 7.323 43925 Z= 0.319 Chirality : 0.046 0.171 5107 Planarity : 0.005 0.075 5890 Dihedral : 5.940 92.701 4837 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.03 % Allowed : 19.42 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4445 helix: 0.52 (0.12), residues: 1839 sheet: -0.36 (0.21), residues: 560 loop : -1.78 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 476 HIS 0.006 0.001 HIS F 735 PHE 0.012 0.002 PHE F 674 TYR 0.019 0.002 TYR D 244 ARG 0.006 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 331 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 GLN cc_start: 0.2578 (OUTLIER) cc_final: 0.1892 (pt0) REVERT: B 639 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 713 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.4223 (ptm-80) REVERT: C 426 LYS cc_start: 0.6620 (mmmm) cc_final: 0.6347 (mtmt) REVERT: C 465 ARG cc_start: 0.7066 (mmp80) cc_final: 0.6557 (ptp-170) REVERT: C 473 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7027 (mm110) REVERT: C 534 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6276 (tm-30) REVERT: C 568 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: C 661 LEU cc_start: 0.7280 (mm) cc_final: 0.6988 (mt) REVERT: C 720 MET cc_start: 0.3720 (tpt) cc_final: 0.3296 (tpt) REVERT: C 723 GLU cc_start: 0.0749 (OUTLIER) cc_final: 0.0309 (tt0) REVERT: C 744 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5706 (ttm170) REVERT: D 283 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: D 336 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6836 (mmtm) REVERT: D 389 LYS cc_start: 0.7359 (tptp) cc_final: 0.6842 (mtmt) REVERT: D 449 MET cc_start: 0.7134 (tpt) cc_final: 0.6931 (tpt) REVERT: D 465 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6157 (ttm170) REVERT: E 402 GLU cc_start: 0.7084 (pt0) cc_final: 0.6670 (pt0) REVERT: E 515 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8769 (tt) REVERT: E 599 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: E 666 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7756 (p) REVERT: E 683 SER cc_start: 0.7241 (p) cc_final: 0.6992 (m) REVERT: E 714 GLN cc_start: 0.2881 (OUTLIER) cc_final: 0.2549 (tp40) REVERT: F 252 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8340 (m) REVERT: F 283 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6497 (mt-10) REVERT: F 479 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7494 (mm) REVERT: F 542 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8438 (mp) REVERT: F 657 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7272 (mm) outliers start: 141 outliers final: 110 residues processed: 440 average time/residue: 0.4140 time to fit residues: 293.3854 Evaluate side-chains 444 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 318 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 713 ARG Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ARG Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 327 GLN B 568 GLN C 340 HIS C 406 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 568 GLN ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32320 Z= 0.183 Angle : 0.585 15.982 43925 Z= 0.287 Chirality : 0.044 0.149 5107 Planarity : 0.004 0.072 5890 Dihedral : 5.657 91.807 4837 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.65 (0.13), residues: 4445 helix: 0.80 (0.12), residues: 1837 sheet: -0.23 (0.21), residues: 561 loop : -1.67 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 454 HIS 0.004 0.001 HIS F 735 PHE 0.016 0.001 PHE E 674 TYR 0.018 0.001 TYR B 244 ARG 0.006 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 343 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 GLN cc_start: 0.2554 (OUTLIER) cc_final: 0.1135 (mt0) REVERT: B 390 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 639 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 713 ARG cc_start: 0.4664 (OUTLIER) cc_final: 0.4339 (ptm-80) REVERT: C 424 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.5914 (ptt-90) REVERT: C 426 LYS cc_start: 0.6526 (mmmm) cc_final: 0.6227 (mtmt) REVERT: C 431 ASP cc_start: 0.2298 (OUTLIER) cc_final: 0.2088 (t0) REVERT: C 465 ARG cc_start: 0.7032 (mmp80) cc_final: 0.6452 (ptm-80) REVERT: C 473 GLN cc_start: 0.7309 (mm-40) cc_final: 0.7005 (mm110) REVERT: C 534 GLU cc_start: 0.6496 (tm-30) cc_final: 0.6227 (tm-30) REVERT: C 661 LEU cc_start: 0.7136 (mm) cc_final: 0.6834 (mt) REVERT: C 720 MET cc_start: 0.3850 (tpt) cc_final: 0.3422 (tpt) REVERT: D 283 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: D 336 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6372 (mmtm) REVERT: D 465 ARG cc_start: 0.6973 (mmp80) cc_final: 0.6145 (ttm170) REVERT: D 625 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7930 (mtp85) REVERT: E 402 GLU cc_start: 0.7054 (pt0) cc_final: 0.6604 (pt0) REVERT: E 666 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7777 (p) REVERT: E 751 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6365 (m-30) REVERT: F 244 TYR cc_start: 0.7761 (p90) cc_final: 0.7420 (p90) REVERT: F 283 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: F 542 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8438 (mp) REVERT: F 657 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7156 (mm) outliers start: 112 outliers final: 80 residues processed: 427 average time/residue: 0.4295 time to fit residues: 293.6828 Evaluate side-chains 414 residues out of total 3797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 322 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 713 ARG Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0768 > 50: distance: 48 - 68: 6.958 distance: 54 - 76: 16.067 distance: 57 - 60: 9.925 distance: 58 - 81: 29.537 distance: 60 - 61: 6.592 distance: 61 - 62: 3.812 distance: 61 - 64: 8.332 distance: 62 - 63: 5.189 distance: 62 - 68: 5.017 distance: 63 - 86: 21.642 distance: 64 - 65: 6.006 distance: 65 - 66: 11.339 distance: 68 - 69: 8.516 distance: 69 - 70: 4.087 distance: 69 - 72: 5.632 distance: 70 - 71: 7.695 distance: 70 - 76: 7.187 distance: 71 - 94: 7.273 distance: 72 - 73: 7.145 distance: 73 - 74: 15.093 distance: 73 - 75: 17.486 distance: 76 - 77: 6.919 distance: 77 - 78: 8.307 distance: 77 - 80: 13.756 distance: 78 - 79: 21.382 distance: 78 - 81: 26.183 distance: 79 - 100: 16.769 distance: 81 - 82: 30.088 distance: 82 - 83: 10.090 distance: 82 - 85: 29.079 distance: 83 - 84: 10.166 distance: 83 - 86: 8.502 distance: 84 - 106: 22.989 distance: 86 - 87: 3.981 distance: 87 - 88: 4.613 distance: 87 - 90: 5.870 distance: 88 - 89: 4.549 distance: 88 - 94: 5.732 distance: 89 - 115: 6.365 distance: 90 - 91: 6.300 distance: 91 - 92: 9.319 distance: 91 - 93: 6.587 distance: 94 - 95: 7.005 distance: 95 - 96: 5.738 distance: 95 - 98: 5.572 distance: 97 - 120: 6.347 distance: 98 - 99: 4.888 distance: 100 - 101: 6.415 distance: 101 - 104: 9.344 distance: 102 - 103: 3.390 distance: 102 - 106: 7.912 distance: 103 - 125: 6.474 distance: 104 - 105: 5.482 distance: 106 - 107: 3.840 distance: 107 - 108: 3.746 distance: 109 - 133: 11.468 distance: 110 - 111: 5.434 distance: 111 - 112: 3.728 distance: 112 - 113: 4.320 distance: 115 - 116: 4.659 distance: 116 - 119: 4.636 distance: 117 - 120: 5.112 distance: 121 - 122: 4.181 distance: 121 - 124: 5.270 distance: 122 - 125: 3.700 distance: 123 - 143: 4.648