Starting phenix.real_space_refine on Mon Apr 15 14:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln5_23449/04_2024/7ln5_23449_updated.pdb" } resolution = 3.09 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= 0.002 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: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21949 2.51 5 N 6220 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 592": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 734": "OD1" <-> "OD2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D ASP 686": "OD1" <-> "OD2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D ASP 734": "OD1" <-> "OD2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E ASP 410": "OD1" <-> "OD2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E ASP 484": "OD1" <-> "OD2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E ASP 734": "OD1" <-> "OD2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ASP 395": "OD1" <-> "OD2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F ASP 609": "OD1" <-> "OD2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F ASP 630": "OD1" <-> "OD2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F GLU 704": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35051 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5784 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5878 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 661} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "A" 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: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.21, per 1000 atoms: 0.52 Number of scatterers: 35051 At special positions: 0 Unit cell: (163.702, 172.206, 137.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 31 15.00 Mg 7 11.99 O 6666 8.00 N 6220 7.00 C 21949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.58 Conformation dependent library (CDL) restraints added in 6.2 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 34 sheets defined 43.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 130 through 139 removed outlier: 4.733A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.345A 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 227 through 232 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.599A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.223A 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 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 547 Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 592 through 613 removed outlier: 3.704A pdb=" N GLY A 595 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 613 " --> pdb=" O GLY A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.541A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.488A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.840A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.171A 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 227 through 233 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 429 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.570A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.556A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 596 through 608 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.628A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.589A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 138 removed outlier: 4.425A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.386A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.598A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 547 removed outlier: 4.227A pdb=" N LEU C 547 " --> pdb=" O GLY C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 554 through 568 Processing helix chain 'C' and resid 579 through 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 596 through 608 Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.517A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.597A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 removed outlier: 3.650A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.313A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 427 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.619A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 554 through 568 removed outlier: 3.655A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 596 through 608 Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.694A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 removed outlier: 3.552A pdb=" N GLU D 712 " --> pdb=" O ARG D 708 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.550A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.732A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 130 through 139 removed outlier: 4.541A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.342A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.771A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 337 removed outlier: 3.918A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.950A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 554 through 568 Processing helix chain 'E' and resid 579 through 581 No H-bonds generated for 'chain 'E' and resid 579 through 581' Processing helix chain 'E' and resid 596 through 610 removed outlier: 3.878A pdb=" N ILE E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.552A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.538A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 765 removed outlier: 3.580A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.669A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 191 through 198 removed outlier: 3.593A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.551A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 233 removed outlier: 3.518A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 610 Processing helix chain 'F' and resid 631 through 634 No H-bonds generated for 'chain 'F' and resid 631 through 634' Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 713 Processing helix chain 'F' and resid 733 through 742 Processing helix chain 'F' and resid 749 through 760 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.455A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.693A pdb=" N ILE A 114 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 4.238A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 8.964A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 56 through 60 Processing sheet with id= H, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.523A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 144 through 146 removed outlier: 3.712A pdb=" N ARG B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 151 through 154 removed outlier: 3.545A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 365 through 368 removed outlier: 9.234A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 641 through 645 removed outlier: 8.434A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.168A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.624A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL C 181 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.123A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 150 through 154 removed outlier: 3.893A pdb=" N ASP C 150 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.771A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.366A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= T, first strand: chain 'D' and resid 38 through 41 removed outlier: 7.331A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.660A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 113 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.806A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.337A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 641 through 644 removed outlier: 8.243A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.171A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.908A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 144 through 146 removed outlier: 3.987A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.199A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.007A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.386A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.557A pdb=" N ILE F 114 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F 116 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.640A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.956A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.581A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3579 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: 14.32 Time building geometry restraints manager: 14.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.58: 35297 1.58 - 1.93: 334 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 2.99: 2 Bond restraints: 35633 Sorted by residual: bond pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 1.332 2.990 -1.658 1.52e-02 4.33e+03 1.19e+04 bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.333 2.932 -1.599 1.56e-02 4.11e+03 1.05e+04 bond pdb=" CB PRO C 774 " pdb=" CG PRO C 774 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.76e+00 bond pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 1.506 1.575 -0.069 3.90e-02 6.57e+02 3.13e+00 bond pdb=" CG MET C 275 " pdb=" SD MET C 275 " ideal model delta sigma weight residual 1.803 1.761 0.042 2.50e-02 1.60e+03 2.86e+00 ... (remaining 35628 not shown) Histogram of bond angle deviations from ideal: 89.02 - 99.19: 14 99.19 - 109.36: 2584 109.36 - 119.54: 28254 119.54 - 129.71: 17193 129.71 - 139.88: 134 Bond angle restraints: 48179 Sorted by residual: angle pdb=" O LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 122.37 89.02 33.35 1.28e+00 6.10e-01 6.79e+02 angle pdb=" C LEU D 464 " pdb=" N ARG D 465 " pdb=" CA ARG D 465 " ideal model delta sigma weight residual 121.94 91.39 30.55 2.00e+00 2.50e-01 2.33e+02 angle pdb=" C LEU E 464 " pdb=" N ARG E 465 " pdb=" CA ARG E 465 " ideal model delta sigma weight residual 121.52 95.53 25.99 2.34e+00 1.83e-01 1.23e+02 angle pdb=" O LEU D 464 " pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 122.06 96.96 25.10 3.24e+00 9.53e-02 6.00e+01 angle pdb=" CA PRO C 774 " pdb=" N PRO C 774 " pdb=" CD PRO C 774 " ideal model delta sigma weight residual 112.00 103.14 8.86 1.40e+00 5.10e-01 4.00e+01 ... (remaining 48174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 21605 33.06 - 66.11: 510 66.11 - 99.17: 96 99.17 - 132.22: 7 132.22 - 165.28: 3 Dihedral angle restraints: 22221 sinusoidal: 9412 harmonic: 12809 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 105.28 -165.28 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 94.87 -154.86 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PA ADP F 902 " pdb=" PB ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 86.24 -146.24 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 22218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3647 0.032 - 0.063: 1056 0.063 - 0.095: 451 0.095 - 0.127: 251 0.127 - 0.158: 14 Chirality restraints: 5419 Sorted by residual: chirality pdb=" CA THR E 613 " pdb=" N THR E 613 " pdb=" C THR E 613 " pdb=" CB THR E 613 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA PHE D 768 " pdb=" N PHE D 768 " pdb=" C PHE D 768 " pdb=" CB PHE D 768 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CB ILE A 206 " pdb=" CA ILE A 206 " pdb=" CG1 ILE A 206 " pdb=" CG2 ILE A 206 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 5416 not shown) Planarity restraints: 6309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.165 2.00e-02 2.50e+03 2.36e-01 5.56e+02 pdb=" C LEU E 464 " -0.397 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.188 2.00e-02 2.50e+03 pdb=" N ARG E 465 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 464 " 0.125 2.00e-02 2.50e+03 1.75e-01 3.07e+02 pdb=" C LEU D 464 " -0.298 2.00e-02 2.50e+03 pdb=" O LEU D 464 " 0.127 2.00e-02 2.50e+03 pdb=" N ARG D 465 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 773 " 0.087 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO C 774 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " 0.066 5.00e-02 4.00e+02 ... (remaining 6306 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 297 2.59 - 3.17: 29408 3.17 - 3.74: 56653 3.74 - 4.32: 79062 4.32 - 4.90: 127032 Nonbonded interactions: 292452 Sorted by model distance: nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.010 2.170 nonbonded pdb=" O LEU A 548 " pdb=" OG SER A 555 " model vdw 2.037 2.440 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 903 " model vdw 2.041 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 2.045 2.170 nonbonded pdb=" O1G ATP E 902 " pdb="MG MG E 903 " model vdw 2.057 2.170 ... (remaining 292447 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 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'B' and (resid 23 through 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 9.160 Check model and map are aligned: 0.520 Set scattering table: 0.350 Process input model: 92.140 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.013 1.658 35633 Z= 0.572 Angle : 0.670 33.352 48179 Z= 0.366 Chirality : 0.041 0.158 5419 Planarity : 0.006 0.236 6309 Dihedral : 15.268 165.277 13905 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.12), residues: 4383 helix: 1.09 (0.12), residues: 1954 sheet: 0.79 (0.20), residues: 639 loop : 0.48 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 551 HIS 0.008 0.001 HIS E 499 PHE 0.021 0.001 PHE A 266 TYR 0.021 0.001 TYR A 755 ARG 0.014 0.001 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.2357 (mpp) cc_final: 0.1712 (mmp) REVERT: A 357 LEU cc_start: 0.7052 (mt) cc_final: 0.6717 (mt) REVERT: F 84 MET cc_start: 0.4420 (tpt) cc_final: 0.4186 (tpt) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.6163 time to fit residues: 288.8889 Evaluate side-chains 179 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 347 optimal weight: 4.9990 chunk 134 optimal weight: 0.0980 chunk 211 optimal weight: 0.9990 chunk 258 optimal weight: 0.0060 chunk 402 optimal weight: 9.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35633 Z= 0.271 Angle : 0.596 10.952 48179 Z= 0.295 Chirality : 0.044 0.182 5419 Planarity : 0.005 0.059 6309 Dihedral : 10.611 170.406 5123 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.56 % Allowed : 5.06 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.47 (0.13), residues: 4387 helix: 1.59 (0.12), residues: 1935 sheet: 0.49 (0.19), residues: 668 loop : 0.66 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 476 HIS 0.006 0.001 HIS A 735 PHE 0.017 0.001 PHE A 363 TYR 0.016 0.001 TYR C 173 ARG 0.008 0.001 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7092 (tmm) REVERT: E 46 MET cc_start: 0.4083 (mmt) cc_final: 0.3095 (mpp) outliers start: 21 outliers final: 11 residues processed: 217 average time/residue: 0.5019 time to fit residues: 177.9196 Evaluate side-chains 184 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 340 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 chunk 435 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 399 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN E 43 GLN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35633 Z= 0.265 Angle : 0.554 10.371 48179 Z= 0.271 Chirality : 0.043 0.158 5419 Planarity : 0.005 0.108 6309 Dihedral : 10.426 169.531 5123 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.70 % Allowed : 7.42 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.57 (0.13), residues: 4387 helix: 1.78 (0.12), residues: 1931 sheet: 0.38 (0.19), residues: 675 loop : 0.66 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 476 HIS 0.004 0.001 HIS A 735 PHE 0.010 0.001 PHE F 563 TYR 0.010 0.001 TYR A 517 ARG 0.014 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6375 (p0) REVERT: B 740 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7074 (tmm) outliers start: 26 outliers final: 12 residues processed: 193 average time/residue: 0.4579 time to fit residues: 147.3293 Evaluate side-chains 174 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 340 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 383 optimal weight: 30.0000 chunk 115 optimal weight: 0.0040 overall best weight: 2.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35633 Z= 0.253 Angle : 0.541 9.344 48179 Z= 0.264 Chirality : 0.043 0.152 5419 Planarity : 0.004 0.055 6309 Dihedral : 10.201 168.491 5123 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.10 % Allowed : 8.79 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.59 (0.13), residues: 4387 helix: 1.82 (0.12), residues: 1948 sheet: 0.39 (0.19), residues: 662 loop : 0.62 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 476 HIS 0.004 0.001 HIS D 115 PHE 0.011 0.001 PHE F 771 TYR 0.017 0.001 TYR A 244 ARG 0.008 0.000 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5372 (tp) REVERT: B 392 ASP cc_start: 0.6540 (OUTLIER) cc_final: 0.6331 (p0) REVERT: B 740 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7078 (tmm) REVERT: F 219 MET cc_start: 0.7197 (mmm) cc_final: 0.6943 (mtp) outliers start: 41 outliers final: 16 residues processed: 192 average time/residue: 0.4204 time to fit residues: 136.8034 Evaluate side-chains 180 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 340 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 chunk 318 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 365 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 218 optimal weight: 0.9990 chunk 384 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35633 Z= 0.180 Angle : 0.514 9.594 48179 Z= 0.251 Chirality : 0.042 0.156 5419 Planarity : 0.004 0.053 6309 Dihedral : 9.922 168.117 5123 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.05 % Allowed : 9.75 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.68 (0.13), residues: 4387 helix: 1.88 (0.12), residues: 1954 sheet: 0.39 (0.19), residues: 672 loop : 0.70 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 476 HIS 0.003 0.001 HIS A 384 PHE 0.011 0.001 PHE C 131 TYR 0.010 0.001 TYR A 173 ARG 0.005 0.000 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.5711 (OUTLIER) cc_final: 0.5364 (tp) REVERT: B 392 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6298 (p0) REVERT: B 740 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7095 (tmm) REVERT: E 456 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7553 (mp) outliers start: 39 outliers final: 22 residues processed: 194 average time/residue: 0.4491 time to fit residues: 144.7928 Evaluate side-chains 185 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 5.9990 chunk 385 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 428 optimal weight: 20.0000 chunk 355 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 406 HIS B 43 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN D 337 GLN D 348 ASN D 384 HIS D 660 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 35633 Z= 0.534 Angle : 0.680 10.307 48179 Z= 0.335 Chirality : 0.046 0.184 5419 Planarity : 0.005 0.059 6309 Dihedral : 10.466 166.034 5123 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.53 % Allowed : 10.45 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4387 helix: 1.60 (0.12), residues: 1936 sheet: 0.25 (0.19), residues: 660 loop : 0.48 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 476 HIS 0.015 0.001 HIS A 735 PHE 0.021 0.002 PHE C 131 TYR 0.013 0.002 TYR E 755 ARG 0.007 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 165 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5996 (tp) REVERT: B 392 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6419 (p0) REVERT: B 740 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7143 (tmm) REVERT: C 199 ASN cc_start: 0.7128 (p0) cc_final: 0.6906 (p0) REVERT: C 287 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7197 (mtp85) REVERT: D 611 MET cc_start: 0.7352 (mmm) cc_final: 0.7036 (mmm) REVERT: E 456 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7702 (mp) outliers start: 57 outliers final: 34 residues processed: 211 average time/residue: 0.4638 time to fit residues: 169.6121 Evaluate side-chains 192 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 chunk 242 optimal weight: 0.7980 chunk 360 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 267 optimal weight: 0.0970 chunk 260 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN E 36 ASN E 90 ASN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35633 Z= 0.149 Angle : 0.529 11.018 48179 Z= 0.257 Chirality : 0.042 0.148 5419 Planarity : 0.004 0.052 6309 Dihedral : 9.946 165.267 5123 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.07 % Allowed : 11.25 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.56 (0.13), residues: 4387 helix: 1.77 (0.12), residues: 1967 sheet: 0.33 (0.20), residues: 654 loop : 0.63 (0.16), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 476 HIS 0.003 0.001 HIS E 183 PHE 0.011 0.001 PHE F 302 TYR 0.020 0.001 TYR A 173 ARG 0.009 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5700 (tp) REVERT: B 392 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.6072 (p0) REVERT: B 740 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: E 456 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7500 (mp) outliers start: 40 outliers final: 25 residues processed: 197 average time/residue: 0.4745 time to fit residues: 158.6685 Evaluate side-chains 185 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 271 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 335 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35633 Z= 0.148 Angle : 0.529 14.120 48179 Z= 0.252 Chirality : 0.042 0.160 5419 Planarity : 0.004 0.054 6309 Dihedral : 9.621 168.215 5123 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.15 % Allowed : 11.50 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.65 (0.13), residues: 4387 helix: 1.84 (0.12), residues: 1958 sheet: 0.44 (0.20), residues: 649 loop : 0.66 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 476 HIS 0.003 0.001 HIS A 384 PHE 0.012 0.001 PHE F 302 TYR 0.012 0.001 TYR A 173 ARG 0.008 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5856 (tp) REVERT: B 740 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7157 (tmm) REVERT: C 287 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6937 (mtp85) REVERT: E 456 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7506 (mp) outliers start: 43 outliers final: 27 residues processed: 197 average time/residue: 0.4871 time to fit residues: 164.6676 Evaluate side-chains 188 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASP Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 373 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 173 optimal weight: 0.0040 chunk 312 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 35633 Z= 0.393 Angle : 0.621 11.128 48179 Z= 0.301 Chirality : 0.044 0.183 5419 Planarity : 0.005 0.050 6309 Dihedral : 10.080 167.068 5123 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.96 % Allowed : 12.14 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.49 (0.13), residues: 4387 helix: 1.77 (0.12), residues: 1942 sheet: 0.27 (0.20), residues: 671 loop : 0.56 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 476 HIS 0.005 0.001 HIS A 499 PHE 0.016 0.002 PHE C 131 TYR 0.011 0.001 TYR E 755 ARG 0.006 0.001 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.6088 (tp) REVERT: B 740 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7188 (tmm) REVERT: C 287 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7048 (mtp85) REVERT: E 456 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7678 (mp) outliers start: 36 outliers final: 29 residues processed: 188 average time/residue: 0.4542 time to fit residues: 146.7659 Evaluate side-chains 187 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 364 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 420 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 441 optimal weight: 10.0000 chunk 406 optimal weight: 7.9990 chunk 351 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 271 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35633 Z= 0.145 Angle : 0.539 13.635 48179 Z= 0.258 Chirality : 0.042 0.163 5419 Planarity : 0.004 0.048 6309 Dihedral : 9.648 166.060 5123 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.78 % Allowed : 12.25 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.63 (0.13), residues: 4387 helix: 1.91 (0.12), residues: 1938 sheet: 0.26 (0.20), residues: 655 loop : 0.63 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 476 HIS 0.003 0.001 HIS E 183 PHE 0.014 0.001 PHE C 131 TYR 0.014 0.001 TYR B 755 ARG 0.006 0.000 ARG A 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.6033 (OUTLIER) cc_final: 0.5732 (tp) REVERT: B 740 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7128 (tmm) REVERT: E 456 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7545 (mp) outliers start: 29 outliers final: 26 residues processed: 180 average time/residue: 0.4648 time to fit residues: 145.1975 Evaluate side-chains 182 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 734 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 374 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 324 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 361 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.097517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059999 restraints weight = 107541.227| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.28 r_work: 0.2754 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35633 Z= 0.218 Angle : 0.546 12.888 48179 Z= 0.261 Chirality : 0.042 0.149 5419 Planarity : 0.004 0.048 6309 Dihedral : 9.641 167.496 5123 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.94 % Allowed : 12.30 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.64 (0.13), residues: 4387 helix: 1.94 (0.12), residues: 1936 sheet: 0.28 (0.20), residues: 655 loop : 0.61 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 476 HIS 0.003 0.001 HIS B 115 PHE 0.012 0.001 PHE F 52 TYR 0.010 0.001 TYR B 755 ARG 0.006 0.000 ARG A 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6635.11 seconds wall clock time: 128 minutes 45.20 seconds (7725.20 seconds total)