Starting phenix.real_space_refine on Sat Mar 23 00:16:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln2_23446/03_2024/7ln2_23446_updated.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21879 2.51 5 N 6200 2.21 5 O 6646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 710": "OE1" <-> "OE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ASP 671": "OD1" <-> "OD2" Residue "D ASP 686": "OD1" <-> "OD2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D GLU 738": "OE1" <-> "OE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 392": "OD1" <-> "OD2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F GLU 710": "OE1" <-> "OE2" Residue "F GLU 730": "OE1" <-> "OE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34941 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 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: 1 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: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 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: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5712 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 692} Chain breaks: 1 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: 5506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5506 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 659} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.12, per 1000 atoms: 0.49 Number of scatterers: 34941 At special positions: 0 Unit cell: (155.434, 172.704, 131.687, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 31 15.00 Mg 7 11.99 O 6646 8.00 N 6200 7.00 C 21879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.66 Conformation dependent library (CDL) restraints added in 5.9 seconds 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 207 helices and 35 sheets defined 43.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.09 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 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 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 320 through 334 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 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.014A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 545 through 548 No H-bonds generated for 'chain 'A' and resid 545 through 548' Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 592 through 611 removed outlier: 3.762A pdb=" N GLY A 595 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 660 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 Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' 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: 4.201A 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 355 through 358 Processing helix chain 'B' and resid 374 through 387 removed outlier: 4.554A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) 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 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 547 removed outlier: 4.118A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 596 through 608 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' 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 713 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 766 Processing helix chain 'C' and resid 13 through 16 removed outlier: 3.616A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 16' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.230A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.587A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 554 through 568 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 596 through 608 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 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 749 through 766 Processing helix chain 'D' and resid 13 through 17 removed outlier: 3.787A pdb=" N ILE D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.085A 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 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.710A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) 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 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 409 through 427 removed outlier: 3.640A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 545 through 547 No H-bonds generated for 'chain 'D' and resid 545 through 547' Processing helix chain 'D' and resid 554 through 568 Processing helix chain 'D' and resid 579 through 582 No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 592 through 608 removed outlier: 6.896A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 No H-bonds generated for 'chain 'D' and resid 631 through 634' 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 Processing helix chain 'D' and resid 749 through 766 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.070A 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 Processing helix chain 'E' and resid 251 through 260 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 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 337 removed outlier: 4.050A 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 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.536A pdb=" N LYS E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 426 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 462 through 467 removed outlier: 4.283A pdb=" N GLU E 466 " --> pdb=" O SER E 462 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 467' 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 Processing helix chain 'E' and resid 524 through 534 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 568 Processing helix chain 'E' and resid 579 through 582 No H-bonds generated for 'chain 'E' and resid 579 through 582' Processing helix chain 'E' and resid 588 through 591 No H-bonds generated for 'chain 'E' and resid 588 through 591' 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 650 through 660 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 742 Processing helix chain 'E' and resid 749 through 765 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 92 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 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.175A 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 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 387 removed outlier: 3.753A 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 409 through 426 removed outlier: 3.651A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 559 through 569 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 613 removed outlier: 3.648A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (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 83 removed outlier: 7.453A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.855A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.838A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.609A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 244 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.515A 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: 3.624A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.589A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.754A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.644A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.659A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 641 through 645 removed outlier: 8.407A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= M, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.656A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP C 55 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.550A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.503A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.294A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= S, first strand: chain 'D' and resid 38 through 41 removed outlier: 7.251A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.030A pdb=" N VAL D 181 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 151 through 154 Processing sheet with id= V, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.350A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 641 through 645 removed outlier: 8.569A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.674A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= Z, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.594A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.845A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 242 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.350A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 27 through 30 Processing sheet with id= AD, first strand: chain 'F' and resid 39 through 41 removed outlier: 3.881A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.949A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AG, first strand: chain 'F' and resid 150 through 154 removed outlier: 3.714A pdb=" N ASP F 150 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.575A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.687A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1252 hydrogen bonds defined for protein. 3648 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: 12.82 Time building geometry restraints manager: 12.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11899 1.34 - 1.46: 4859 1.46 - 1.58: 18448 1.58 - 1.70: 34 1.70 - 1.82: 284 Bond restraints: 35524 Sorted by residual: bond pdb=" CB PRO F 519 " pdb=" CG PRO F 519 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.12e+00 bond pdb=" CB PRO A 472 " pdb=" CG PRO A 472 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 bond pdb=" N PHE B 768 " pdb=" CA PHE B 768 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.29e+00 bond pdb=" CA THR B 448 " pdb=" CB THR B 448 " ideal model delta sigma weight residual 1.534 1.560 -0.025 1.77e-02 3.19e+03 2.07e+00 bond pdb=" CB ILE B 582 " pdb=" CG2 ILE B 582 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 ... (remaining 35519 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.39: 941 105.39 - 113.97: 20704 113.97 - 122.55: 22194 122.55 - 131.13: 4095 131.13 - 139.71: 100 Bond angle restraints: 48034 Sorted by residual: angle pdb=" CA PRO F 519 " pdb=" N PRO F 519 " pdb=" CD PRO F 519 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" N PRO F 519 " pdb=" CD PRO F 519 " pdb=" CG PRO F 519 " ideal model delta sigma weight residual 103.20 97.74 5.46 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C ASP C 431 " pdb=" N LEU C 432 " pdb=" CA LEU C 432 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 118.44 123.96 -5.52 1.59e+00 3.96e-01 1.21e+01 angle pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 118.44 123.94 -5.50 1.59e+00 3.96e-01 1.20e+01 ... (remaining 48029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 21330 29.31 - 58.61: 725 58.61 - 87.92: 84 87.92 - 117.23: 9 117.23 - 146.53: 5 Dihedral angle restraints: 22153 sinusoidal: 9384 harmonic: 12769 Sorted by residual: dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 86.53 -146.53 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 77.28 -137.28 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.33 -132.32 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 22150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3579 0.035 - 0.069: 1168 0.069 - 0.104: 454 0.104 - 0.139: 190 0.139 - 0.173: 9 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CB ILE F 82 " pdb=" CA ILE F 82 " pdb=" CG1 ILE F 82 " pdb=" CG2 ILE F 82 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ILE F 151 " pdb=" N ILE F 151 " pdb=" C ILE F 151 " pdb=" CB ILE F 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 5397 not shown) Planarity restraints: 6291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 518 " -0.067 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO F 519 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO F 519 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 519 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 773 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.24e+00 pdb=" N PRO C 774 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO C 545 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.035 5.00e-02 4.00e+02 ... (remaining 6288 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 255 2.57 - 3.15: 28842 3.15 - 3.73: 56016 3.73 - 4.32: 76508 4.32 - 4.90: 124011 Nonbonded interactions: 285632 Sorted by model distance: nonbonded pdb=" O1G ATP C 901 " pdb="MG MG C 903 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 1.989 2.170 nonbonded pdb=" O2B ATP C 901 " pdb="MG MG C 903 " model vdw 1.994 2.170 nonbonded pdb=" O1G ATP E 902 " pdb="MG MG E 904 " model vdw 2.000 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 903 " model vdw 2.043 2.170 ... (remaining 285627 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 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 533 or (resid 5 \ 34 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 8.840 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 85.960 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 35524 Z= 0.266 Angle : 0.650 12.781 48034 Z= 0.346 Chirality : 0.043 0.173 5400 Planarity : 0.005 0.094 6291 Dihedral : 14.331 146.534 13865 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.50 (0.12), residues: 4377 helix: 1.50 (0.12), residues: 1955 sheet: 1.14 (0.19), residues: 639 loop : 0.51 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 454 HIS 0.009 0.001 HIS B 115 PHE 0.023 0.002 PHE F 290 TYR 0.020 0.002 TYR D 244 ARG 0.014 0.001 ARG E 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 MET cc_start: -0.0702 (tmm) cc_final: -0.1429 (ptm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.4995 time to fit residues: 196.6700 Evaluate side-chains 147 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 7.9990 chunk 335 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 257 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 568 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN C 660 ASN D 19 GLN D 533 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35524 Z= 0.249 Angle : 0.599 9.574 48034 Z= 0.299 Chirality : 0.042 0.200 5400 Planarity : 0.004 0.058 6291 Dihedral : 10.053 136.674 5110 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.46 % Allowed : 5.35 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.75 (0.13), residues: 4377 helix: 1.85 (0.12), residues: 1943 sheet: 0.92 (0.19), residues: 667 loop : 0.62 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.012 0.001 HIS F 340 PHE 0.016 0.001 PHE A 152 TYR 0.014 0.001 TYR D 755 ARG 0.011 0.000 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 158 MET cc_start: 0.3911 (ppp) cc_final: 0.3319 (pmm) REVERT: E 46 MET cc_start: -0.0957 (tmm) cc_final: -0.1270 (ptm) REVERT: E 335 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6360 (tt) outliers start: 17 outliers final: 10 residues processed: 160 average time/residue: 0.4465 time to fit residues: 122.4204 Evaluate side-chains 148 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 434 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 398 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN B 641 GLN C 19 GLN C 458 GLN C 533 ASN D 602 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35524 Z= 0.371 Angle : 0.647 9.797 48034 Z= 0.325 Chirality : 0.043 0.228 5400 Planarity : 0.005 0.057 6291 Dihedral : 9.878 128.414 5110 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 0.86 % Allowed : 8.15 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.60 (0.13), residues: 4377 helix: 1.65 (0.12), residues: 1968 sheet: 0.88 (0.20), residues: 641 loop : 0.61 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 476 HIS 0.006 0.001 HIS C 499 PHE 0.016 0.002 PHE F 771 TYR 0.015 0.001 TYR A 495 ARG 0.018 0.001 ARG E 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 4.323 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: E 508 MET cc_start: 0.6790 (mpp) cc_final: 0.6198 (mmm) REVERT: F 757 MET cc_start: 0.7231 (ppp) cc_final: 0.6903 (ppp) outliers start: 32 outliers final: 17 residues processed: 158 average time/residue: 0.4351 time to fit residues: 118.6827 Evaluate side-chains 144 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 chunk 427 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 382 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35524 Z= 0.173 Angle : 0.538 9.573 48034 Z= 0.265 Chirality : 0.042 0.197 5400 Planarity : 0.004 0.053 6291 Dihedral : 9.220 122.479 5110 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer: Outliers : 1.02 % Allowed : 9.25 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 4377 helix: 1.88 (0.12), residues: 1961 sheet: 1.03 (0.20), residues: 628 loop : 0.65 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 454 HIS 0.003 0.001 HIS F 340 PHE 0.018 0.001 PHE F 674 TYR 0.010 0.001 TYR F 517 ARG 0.009 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 3.694 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: E 508 MET cc_start: 0.6601 (mpp) cc_final: 0.6047 (mmm) outliers start: 38 outliers final: 13 residues processed: 164 average time/residue: 0.4195 time to fit residues: 120.8394 Evaluate side-chains 142 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 318 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 218 optimal weight: 0.9980 chunk 383 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35524 Z= 0.316 Angle : 0.589 9.796 48034 Z= 0.293 Chirality : 0.041 0.187 5400 Planarity : 0.004 0.052 6291 Dihedral : 9.046 117.181 5110 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 1.10 % Allowed : 10.51 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.79 (0.13), residues: 4377 helix: 1.85 (0.12), residues: 1959 sheet: 1.05 (0.20), residues: 620 loop : 0.64 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 454 HIS 0.005 0.001 HIS B 404 PHE 0.024 0.001 PHE F 674 TYR 0.010 0.001 TYR A 495 ARG 0.005 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 508 MET cc_start: 0.6576 (mpp) cc_final: 0.6011 (mmm) outliers start: 41 outliers final: 23 residues processed: 155 average time/residue: 0.4369 time to fit residues: 117.7880 Evaluate side-chains 148 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 250 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 427 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 224 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN F 602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35524 Z= 0.299 Angle : 0.595 18.189 48034 Z= 0.294 Chirality : 0.042 0.185 5400 Planarity : 0.004 0.052 6291 Dihedral : 8.790 112.067 5110 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Rotamer: Outliers : 1.32 % Allowed : 11.19 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.72 (0.13), residues: 4377 helix: 1.77 (0.12), residues: 1957 sheet: 1.06 (0.21), residues: 614 loop : 0.62 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.006 0.001 HIS B 404 PHE 0.018 0.001 PHE F 674 TYR 0.012 0.001 TYR E 173 ARG 0.012 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 508 MET cc_start: 0.5902 (mpp) cc_final: 0.5266 (mmm) outliers start: 49 outliers final: 31 residues processed: 165 average time/residue: 0.4286 time to fit residues: 123.4087 Evaluate side-chains 154 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 238 optimal weight: 0.0070 chunk 426 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 196 optimal weight: 0.0570 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35524 Z= 0.146 Angle : 0.541 13.220 48034 Z= 0.263 Chirality : 0.042 0.190 5400 Planarity : 0.004 0.052 6291 Dihedral : 8.424 109.939 5110 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer: Outliers : 0.91 % Allowed : 11.80 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.91 (0.13), residues: 4377 helix: 1.97 (0.12), residues: 1964 sheet: 1.07 (0.20), residues: 634 loop : 0.69 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.003 0.001 HIS B 404 PHE 0.037 0.001 PHE F 674 TYR 0.009 0.001 TYR E 173 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 508 MET cc_start: 0.6077 (mpp) cc_final: 0.5539 (mmm) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 0.4235 time to fit residues: 115.4565 Evaluate side-chains 149 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 270 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35524 Z= 0.230 Angle : 0.580 13.216 48034 Z= 0.282 Chirality : 0.041 0.212 5400 Planarity : 0.004 0.051 6291 Dihedral : 8.339 107.751 5110 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 0.91 % Allowed : 12.15 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.93 (0.13), residues: 4377 helix: 1.98 (0.12), residues: 1961 sheet: 1.17 (0.21), residues: 617 loop : 0.67 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 454 HIS 0.004 0.001 HIS B 404 PHE 0.028 0.001 PHE F 674 TYR 0.010 0.001 TYR E 173 ARG 0.005 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 3.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 508 MET cc_start: 0.6020 (mpp) cc_final: 0.5487 (mmm) REVERT: E 608 MET cc_start: 0.6461 (ppp) cc_final: 0.5961 (ptm) outliers start: 34 outliers final: 28 residues processed: 152 average time/residue: 0.4498 time to fit residues: 119.0059 Evaluate side-chains 152 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 30.0000 chunk 408 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 172 optimal weight: 5.9990 chunk 311 optimal weight: 40.0000 chunk 121 optimal weight: 0.0570 chunk 358 optimal weight: 6.9990 chunk 375 optimal weight: 7.9990 chunk 395 optimal weight: 7.9990 overall best weight: 5.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 35524 Z= 0.376 Angle : 0.681 12.184 48034 Z= 0.335 Chirality : 0.043 0.266 5400 Planarity : 0.004 0.052 6291 Dihedral : 8.615 105.421 5110 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.40 % Rotamer: Outliers : 1.16 % Allowed : 12.26 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.62 (0.13), residues: 4377 helix: 1.70 (0.12), residues: 1966 sheet: 0.82 (0.20), residues: 640 loop : 0.60 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 454 HIS 0.006 0.001 HIS B 404 PHE 0.032 0.002 PHE F 674 TYR 0.012 0.001 TYR A 495 ARG 0.006 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 608 MET cc_start: 0.6431 (ppp) cc_final: 0.5988 (ptm) outliers start: 43 outliers final: 35 residues processed: 159 average time/residue: 0.4239 time to fit residues: 117.3788 Evaluate side-chains 159 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 440 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35524 Z= 0.229 Angle : 0.602 13.076 48034 Z= 0.294 Chirality : 0.042 0.242 5400 Planarity : 0.004 0.054 6291 Dihedral : 8.408 105.680 5110 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 0.97 % Allowed : 12.77 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 4377 helix: 1.84 (0.12), residues: 1959 sheet: 0.88 (0.20), residues: 638 loop : 0.68 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 454 HIS 0.005 0.001 HIS B 404 PHE 0.016 0.001 PHE E 758 TYR 0.010 0.001 TYR E 173 ARG 0.011 0.000 ARG A 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 608 MET cc_start: 0.6439 (ppp) cc_final: 0.6012 (ptm) outliers start: 36 outliers final: 31 residues processed: 153 average time/residue: 0.4346 time to fit residues: 115.7185 Evaluate side-chains 155 residues out of total 3770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 5.9990 chunk 373 optimal weight: 50.0000 chunk 107 optimal weight: 0.6980 chunk 323 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 351 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 360 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.1038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.074038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043841 restraints weight = 226563.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.044087 restraints weight = 125852.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044606 restraints weight = 88078.431| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35524 Z= 0.151 Angle : 0.577 13.177 48034 Z= 0.280 Chirality : 0.042 0.236 5400 Planarity : 0.004 0.052 6291 Dihedral : 8.068 105.877 5110 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 0.94 % Allowed : 12.72 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 4377 helix: 1.91 (0.12), residues: 1960 sheet: 0.94 (0.20), residues: 639 loop : 0.76 (0.16), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 454 HIS 0.003 0.001 HIS D 226 PHE 0.016 0.001 PHE B 771 TYR 0.010 0.001 TYR E 173 ARG 0.007 0.000 ARG A 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.69 seconds wall clock time: 98 minutes 52.57 seconds (5932.57 seconds total)