Starting phenix.real_space_refine on Thu Feb 22 19:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln4_23448/02_2024/7ln4_23448_updated.pdb" } resolution = 3.0 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 32 5.49 5 Mg 8 5.21 5 S 178 5.16 5 C 21971 2.51 5 N 6227 2.21 5 O 6678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B ASP 598": "OD1" <-> "OD2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E ASP 395": "OD1" <-> "OD2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E ASP 484": "OD1" <-> "OD2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F ASP 577": "OD1" <-> "OD2" Residue "F PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 649": "OD1" <-> "OD2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F ASP 686": "OD1" <-> "OD2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F ASP 751": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35094 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5707 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5858 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 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: 5862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5862 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 709} Chain breaks: 3 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: "E" Number of atoms: 5796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5796 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 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: 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: "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: 18.83, per 1000 atoms: 0.54 Number of scatterers: 35094 At special positions: 0 Unit cell: (162.989, 171.625, 136.004, 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 32 15.00 Mg 8 11.99 O 6678 8.00 N 6227 7.00 C 21971 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: 13.34 Conformation dependent library (CDL) restraints added in 6.4 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 32 sheets defined 43.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.16 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 92 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: 4.597A 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 199 removed outlier: 3.821A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.422A 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 233 removed outlier: 4.019A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 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 333 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.169A 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 535 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 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 594 through 613 removed outlier: 4.172A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 removed outlier: 4.746A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) 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: 3.572A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 766 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 91 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 139 removed outlier: 4.644A 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 198 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: 4.039A 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 332 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 427 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.585A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) 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: 3.559A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.559A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 608 removed outlier: 3.513A pdb=" N ILE B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) 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 661 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 696 Processing helix chain 'B' and resid 699 through 713 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.734A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.846A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 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 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 130 through 139 removed outlier: 4.573A 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: 4.203A 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 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 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 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 429 removed outlier: 3.709A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.772A 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 removed outlier: 3.585A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 547 removed outlier: 3.990A 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 removed outlier: 3.597A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 593 through 608 removed outlier: 3.502A pdb=" N ALA C 596 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 597 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET C 608 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 removed outlier: 3.504A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.821A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 765 removed outlier: 3.668A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 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 139 removed outlier: 4.699A 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 225 removed outlier: 4.067A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 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 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 386 removed outlier: 3.502A pdb=" N LYS D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 463 through 466 removed outlier: 4.660A pdb=" N GLU D 466 " --> pdb=" O ALA D 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 463 through 466' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.720A 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 removed outlier: 3.679A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) 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: 3.519A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.607A pdb=" N ILE D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.605A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.779A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 43 through 48 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 92 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: 4.611A 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: 3.849A 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: 3.686A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 274 No H-bonds generated for 'chain 'E' and resid 271 through 274' Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.712A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) 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 338 removed outlier: 3.922A 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 386 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 430 removed outlier: 4.418A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (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 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.550A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.705A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 547 No H-bonds generated for 'chain 'E' and resid 545 through 547' Processing helix chain 'E' and resid 554 through 569 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 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 No H-bonds generated for 'chain 'E' and resid 631 through 634' Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.658A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.767A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 765 removed outlier: 3.556A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.737A 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 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.507A 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 199 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: 4.365A 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 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 374 through 387 removed outlier: 4.491A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) 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 535 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 612 removed outlier: 3.567A pdb=" N MET F 611 " --> pdb=" O GLU F 607 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER F 612 " --> pdb=" O MET F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' 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 761 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.465A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.345A 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: 7.005A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.548A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 369 removed outlier: 3.833A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.543A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.460A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.809A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.591A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.787A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 644 removed outlier: 8.566A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.491A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.524A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.605A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 644 removed outlier: 8.422A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.617A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.512A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.559A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.208A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 644 removed outlier: 8.431A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.598A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.912A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.612A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.225A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= AA, first strand: chain 'F' and resid 38 through 41 removed outlier: 7.396A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 167 through 169 removed outlier: 3.511A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 113 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.957A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 151 through 154 removed outlier: 3.519A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 365 through 369 removed outlier: 6.407A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLY F 245 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR F 347 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 641 through 644 removed outlier: 6.960A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.55 Time building geometry restraints manager: 14.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 35330 1.57 - 1.92: 339 1.92 - 2.26: 0 2.26 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 35670 Sorted by residual: bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.333 2.958 -1.625 1.47e-02 4.63e+03 1.22e+04 bond pdb=" CG PRO E 636 " pdb=" CD PRO E 636 " ideal model delta sigma weight residual 1.503 1.362 0.141 3.40e-02 8.65e+02 1.72e+01 bond pdb=" CB PRO F 461 " pdb=" CG PRO F 461 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+01 bond pdb=" CB PRO E 636 " pdb=" CG PRO E 636 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CG PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 1.503 1.393 0.110 3.40e-02 8.65e+02 1.05e+01 ... (remaining 35665 not shown) Histogram of bond angle deviations from ideal: 78.35 - 90.66: 1 90.66 - 102.97: 289 102.97 - 115.27: 22754 115.27 - 127.58: 24895 127.58 - 139.88: 288 Bond angle restraints: 48227 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 122.83 78.35 44.48 1.35e+00 5.49e-01 1.09e+03 angle pdb=" CA LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 116.11 95.46 20.65 1.30e+00 5.92e-01 2.52e+02 angle pdb=" C LEU E 464 " pdb=" N ARG E 465 " pdb=" CA ARG E 465 " ideal model delta sigma weight residual 122.26 97.10 25.16 1.73e+00 3.34e-01 2.11e+02 angle pdb=" CA PRO E 636 " pdb=" N PRO E 636 " pdb=" CD PRO E 636 " ideal model delta sigma weight residual 112.00 94.42 17.58 1.40e+00 5.10e-01 1.58e+02 angle pdb=" CA PRO F 461 " pdb=" N PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 112.00 95.26 16.74 1.40e+00 5.10e-01 1.43e+02 ... (remaining 48222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 21812 33.37 - 66.74: 393 66.74 - 100.11: 60 100.11 - 133.47: 3 133.47 - 166.84: 4 Dihedral angle restraints: 22272 sinusoidal: 9442 harmonic: 12830 Sorted by residual: 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 300.00 133.16 166.84 1 2.00e+01 2.50e-03 4.74e+01 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 -60.00 102.15 -162.15 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 81.89 -141.89 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4432 0.051 - 0.103: 807 0.103 - 0.154: 191 0.154 - 0.206: 0 0.206 - 0.257: 1 Chirality restraints: 5431 Sorted by residual: chirality pdb=" CA PRO E 636 " pdb=" N PRO E 636 " pdb=" C PRO E 636 " pdb=" CB PRO E 636 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E 123 " pdb=" CA VAL E 123 " pdb=" CG1 VAL E 123 " pdb=" CG2 VAL E 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 5428 not shown) Planarity restraints: 6311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.186 2.00e-02 2.50e+03 2.72e-01 7.40e+02 pdb=" C LEU E 464 " -0.444 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.254 2.00e-02 2.50e+03 pdb=" N ARG E 465 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 635 " -0.106 5.00e-02 4.00e+02 1.44e-01 3.31e+01 pdb=" N PRO E 636 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO E 636 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 636 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.104 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO F 461 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.073 5.00e-02 4.00e+02 ... (remaining 6308 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 273 2.60 - 3.17: 29430 3.17 - 3.75: 55205 3.75 - 4.32: 76529 4.32 - 4.90: 124525 Nonbonded interactions: 285962 Sorted by model distance: nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 903 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 2.059 2.170 nonbonded pdb=" O LEU A 548 " pdb=" OG SER A 555 " model vdw 2.063 2.440 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 903 " model vdw 2.063 2.170 ... (remaining 285957 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 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 53 \ 5 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'B' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 461 or resid 472 t \ hrough 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 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'D' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'E' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'F' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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: 2.200 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: 9.120 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 89.880 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.009 1.625 35670 Z= 0.763 Angle : 0.651 44.476 48227 Z= 0.378 Chirality : 0.042 0.257 5431 Planarity : 0.006 0.272 6311 Dihedral : 13.673 166.843 13938 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.79 % 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: 4386 helix: 1.36 (0.12), residues: 1928 sheet: 1.62 (0.20), residues: 666 loop : 0.48 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 476 HIS 0.008 0.001 HIS A 406 PHE 0.020 0.001 PHE F 575 TYR 0.022 0.001 TYR F 495 ARG 0.009 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 4.423 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 outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 1.8981 time to fit residues: 560.5691 Evaluate side-chains 152 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 336 optimal weight: 0.0020 chunk 186 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 348 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 403 optimal weight: 5.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 421 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 43 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35670 Z= 0.218 Angle : 0.547 7.186 48227 Z= 0.275 Chirality : 0.043 0.265 5431 Planarity : 0.004 0.073 6311 Dihedral : 10.402 174.910 5150 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.88 % Allowed : 5.35 % Favored : 93.76 % 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: 1.77 (0.13), residues: 4388 helix: 1.75 (0.12), residues: 1918 sheet: 1.27 (0.19), residues: 700 loop : 0.64 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 454 HIS 0.003 0.001 HIS A 183 PHE 0.016 0.001 PHE C 131 TYR 0.027 0.001 TYR F 143 ARG 0.010 0.000 ARG E 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 3.948 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: A 84 MET cc_start: -0.2026 (ttt) cc_final: -0.2286 (ttt) REVERT: D 219 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6403 (mtt) REVERT: E 388 MET cc_start: 0.6843 (mtt) cc_final: 0.6631 (mtm) REVERT: F 46 MET cc_start: -0.1116 (ptm) cc_final: -0.1337 (ttp) REVERT: F 499 HIS cc_start: 0.3313 (OUTLIER) cc_final: 0.3093 (m-70) outliers start: 33 outliers final: 11 residues processed: 173 average time/residue: 1.6880 time to fit residues: 346.0206 Evaluate side-chains 158 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.0970 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 436 optimal weight: 10.0000 chunk 359 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN E 215 GLN E 226 HIS E 538 ASN F 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35670 Z= 0.258 Angle : 0.548 9.401 48227 Z= 0.272 Chirality : 0.043 0.154 5431 Planarity : 0.004 0.056 6311 Dihedral : 10.031 168.814 5150 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 0.96 % Allowed : 6.77 % Favored : 92.26 % 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: 1.82 (0.13), residues: 4388 helix: 1.89 (0.12), residues: 1913 sheet: 1.23 (0.20), residues: 685 loop : 0.57 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.009 0.001 HIS F 384 PHE 0.014 0.001 PHE F 575 TYR 0.026 0.001 TYR F 143 ARG 0.009 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6244 (mtt) REVERT: E 158 MET cc_start: 0.4071 (OUTLIER) cc_final: 0.3834 (pmm) REVERT: E 388 MET cc_start: 0.6815 (mtt) cc_final: 0.6613 (mtm) REVERT: F 499 HIS cc_start: 0.3486 (OUTLIER) cc_final: 0.3239 (m-70) outliers start: 36 outliers final: 11 residues processed: 171 average time/residue: 1.6547 time to fit residues: 336.6511 Evaluate side-chains 154 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 6.9990 chunk 429 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN E 215 GLN F 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35670 Z= 0.327 Angle : 0.575 7.332 48227 Z= 0.285 Chirality : 0.044 0.160 5431 Planarity : 0.004 0.060 6311 Dihedral : 9.843 148.457 5148 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % Rotamer: Outliers : 1.07 % Allowed : 8.30 % Favored : 90.63 % 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: 1.82 (0.13), residues: 4388 helix: 1.96 (0.12), residues: 1900 sheet: 1.14 (0.20), residues: 685 loop : 0.55 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.004 0.001 HIS B 499 PHE 0.021 0.001 PHE F 674 TYR 0.021 0.001 TYR F 143 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6264 (mtt) REVERT: E 158 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.3806 (pmm) REVERT: F 499 HIS cc_start: 0.3638 (OUTLIER) cc_final: 0.3375 (m-70) outliers start: 40 outliers final: 14 residues processed: 169 average time/residue: 1.6347 time to fit residues: 328.5487 Evaluate side-chains 159 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 366 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 219 optimal weight: 4.9990 chunk 385 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35670 Z= 0.196 Angle : 0.546 11.268 48227 Z= 0.264 Chirality : 0.042 0.150 5431 Planarity : 0.004 0.059 6311 Dihedral : 9.487 144.806 5148 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 0.88 % Allowed : 9.42 % Favored : 89.69 % 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: 1.87 (0.13), residues: 4388 helix: 2.01 (0.12), residues: 1903 sheet: 1.14 (0.20), residues: 689 loop : 0.56 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 551 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE F 674 TYR 0.019 0.001 TYR F 143 ARG 0.009 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.4056 (OUTLIER) cc_final: 0.3790 (pmm) REVERT: F 499 HIS cc_start: 0.3610 (OUTLIER) cc_final: 0.3349 (m-70) outliers start: 33 outliers final: 15 residues processed: 167 average time/residue: 1.6473 time to fit residues: 328.0155 Evaluate side-chains 159 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 7.9990 chunk 386 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 251 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 429 optimal weight: 30.0000 chunk 356 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 327 GLN E 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35670 Z= 0.387 Angle : 0.615 9.371 48227 Z= 0.301 Chirality : 0.044 0.161 5431 Planarity : 0.004 0.062 6311 Dihedral : 9.567 143.476 5148 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 9.98 % Favored : 88.84 % 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: 1.77 (0.13), residues: 4388 helix: 1.97 (0.12), residues: 1895 sheet: 1.01 (0.20), residues: 680 loop : 0.51 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 551 HIS 0.006 0.001 HIS B 499 PHE 0.020 0.001 PHE F 674 TYR 0.018 0.001 TYR F 143 ARG 0.012 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7467 (p) REVERT: C 275 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.5985 (mmm) REVERT: D 219 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6324 (mtt) REVERT: E 158 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3839 (pmm) REVERT: F 499 HIS cc_start: 0.3511 (OUTLIER) cc_final: 0.3197 (m-70) outliers start: 44 outliers final: 18 residues processed: 174 average time/residue: 1.5878 time to fit residues: 331.2369 Evaluate side-chains 163 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 361 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 427 optimal weight: 30.0000 chunk 267 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35670 Z= 0.180 Angle : 0.568 10.706 48227 Z= 0.274 Chirality : 0.042 0.185 5431 Planarity : 0.004 0.058 6311 Dihedral : 9.168 140.439 5148 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.77 % Rotamer: Outliers : 0.88 % Allowed : 10.87 % Favored : 88.25 % 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: 1.88 (0.13), residues: 4388 helix: 2.09 (0.12), residues: 1888 sheet: 1.00 (0.20), residues: 691 loop : 0.57 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 551 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE F 674 TYR 0.018 0.001 TYR F 143 ARG 0.013 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.3401 (mtt) cc_final: 0.3105 (mtt) REVERT: C 84 MET cc_start: 0.6882 (tmm) cc_final: 0.6163 (tmt) REVERT: C 275 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.5982 (mmm) REVERT: E 158 MET cc_start: 0.4043 (OUTLIER) cc_final: 0.3786 (pmm) REVERT: F 499 HIS cc_start: 0.3681 (OUTLIER) cc_final: 0.3359 (m-70) outliers start: 33 outliers final: 20 residues processed: 162 average time/residue: 1.7290 time to fit residues: 333.3945 Evaluate side-chains 162 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.4980 chunk 170 optimal weight: 0.0970 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 82 optimal weight: 0.0470 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 336 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35670 Z= 0.160 Angle : 0.564 11.791 48227 Z= 0.270 Chirality : 0.042 0.161 5431 Planarity : 0.004 0.058 6311 Dihedral : 8.902 138.257 5148 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 0.72 % Allowed : 11.38 % Favored : 87.90 % 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: 1.92 (0.13), residues: 4388 helix: 2.12 (0.12), residues: 1886 sheet: 1.02 (0.20), residues: 691 loop : 0.58 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 551 HIS 0.003 0.001 HIS B 183 PHE 0.020 0.001 PHE F 674 TYR 0.017 0.001 TYR F 143 ARG 0.010 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.1722 (ttt) cc_final: -0.1989 (ttt) REVERT: A 388 MET cc_start: 0.3592 (mtt) cc_final: 0.3272 (mtt) REVERT: C 86 ARG cc_start: 0.6713 (mmp80) cc_final: 0.6491 (mmp80) REVERT: C 275 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.5978 (mmm) REVERT: E 158 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3904 (pmm) REVERT: E 388 MET cc_start: 0.6871 (mtm) cc_final: 0.6636 (mtm) REVERT: F 499 HIS cc_start: 0.3598 (OUTLIER) cc_final: 0.3306 (m-70) outliers start: 27 outliers final: 16 residues processed: 165 average time/residue: 1.7536 time to fit residues: 343.5293 Evaluate side-chains 160 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.5980 chunk 409 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 398 optimal weight: 0.9980 chunk 240 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35670 Z= 0.207 Angle : 0.590 12.461 48227 Z= 0.281 Chirality : 0.042 0.175 5431 Planarity : 0.004 0.063 6311 Dihedral : 8.818 136.962 5148 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 0.78 % Allowed : 11.43 % Favored : 87.79 % 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: 1.94 (0.13), residues: 4388 helix: 2.13 (0.12), residues: 1886 sheet: 1.03 (0.20), residues: 690 loop : 0.61 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 551 HIS 0.003 0.001 HIS E 183 PHE 0.020 0.001 PHE F 674 TYR 0.017 0.001 TYR F 143 ARG 0.018 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 4.496 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: A 249 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.7293 (p) REVERT: A 388 MET cc_start: 0.3733 (mtt) cc_final: 0.3443 (mtt) REVERT: C 84 MET cc_start: 0.6544 (tmm) cc_final: 0.6010 (tmt) REVERT: C 275 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.5970 (mmm) REVERT: E 158 MET cc_start: 0.4248 (OUTLIER) cc_final: 0.3890 (pmm) REVERT: E 388 MET cc_start: 0.7055 (mtm) cc_final: 0.6847 (mtm) REVERT: F 499 HIS cc_start: 0.3592 (OUTLIER) cc_final: 0.3304 (m-70) outliers start: 29 outliers final: 18 residues processed: 162 average time/residue: 1.7838 time to fit residues: 342.7260 Evaluate side-chains 164 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 5.9990 chunk 421 optimal weight: 9.9990 chunk 257 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 442 optimal weight: 10.0000 chunk 407 optimal weight: 0.1980 chunk 352 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 272 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35670 Z= 0.144 Angle : 0.586 13.363 48227 Z= 0.280 Chirality : 0.042 0.165 5431 Planarity : 0.004 0.066 6311 Dihedral : 8.529 133.682 5148 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 0.64 % Allowed : 11.80 % Favored : 87.55 % 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: 1.95 (0.13), residues: 4388 helix: 2.13 (0.12), residues: 1885 sheet: 1.07 (0.20), residues: 689 loop : 0.61 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 551 HIS 0.003 0.001 HIS C 115 PHE 0.020 0.001 PHE F 674 TYR 0.017 0.001 TYR F 143 ARG 0.021 0.000 ARG C 711 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 4.112 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: A 84 MET cc_start: -0.1713 (ttt) cc_final: -0.1933 (ttt) REVERT: A 249 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7192 (p) REVERT: A 388 MET cc_start: 0.3610 (mtt) cc_final: 0.3291 (mtt) REVERT: B 449 MET cc_start: 0.7956 (mmm) cc_final: 0.7731 (tpp) REVERT: C 84 MET cc_start: 0.6479 (tmm) cc_final: 0.5935 (tmt) REVERT: E 46 MET cc_start: 0.0676 (pmm) cc_final: -0.1123 (ptp) REVERT: E 158 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3842 (pmm) REVERT: E 388 MET cc_start: 0.6870 (mtm) cc_final: 0.6646 (mtm) REVERT: F 499 HIS cc_start: 0.3538 (OUTLIER) cc_final: 0.3254 (m-70) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 1.7155 time to fit residues: 333.5539 Evaluate side-chains 157 residues out of total 3791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 324 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 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 = 0.4131 r_free = 0.4131 target = 0.118951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067540 restraints weight = 100839.412| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.61 r_work: 0.2725 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35670 Z= 0.266 Angle : 0.613 13.306 48227 Z= 0.294 Chirality : 0.043 0.175 5431 Planarity : 0.004 0.108 6311 Dihedral : 8.687 133.590 5148 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 0.75 % Allowed : 11.72 % Favored : 87.53 % 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: 1.92 (0.13), residues: 4388 helix: 2.09 (0.12), residues: 1891 sheet: 1.07 (0.20), residues: 689 loop : 0.59 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 551 HIS 0.003 0.001 HIS B 499 PHE 0.019 0.001 PHE F 674 TYR 0.017 0.001 TYR F 143 ARG 0.012 0.000 ARG B 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8832.06 seconds wall clock time: 159 minutes 32.29 seconds (9572.29 seconds total)