Starting phenix.real_space_refine on Thu Feb 22 18:43:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln0_23444/02_2024/7ln0_23444_updated.pdb" } resolution = 2.98 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21902 2.51 5 N 6208 2.21 5 O 6656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C ASP 686": "OD1" <-> "OD2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "D GLU 738": "OE1" <-> "OE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 671": "OD1" <-> "OD2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34983 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5793 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 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: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} 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: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 661} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.30, per 1000 atoms: 0.49 Number of scatterers: 34983 At special positions: 0 Unit cell: (164.765, 171.143, 132.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 32 15.00 Mg 7 11.99 O 6656 8.00 N 6208 7.00 C 21902 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: 14.30 Conformation dependent library (CDL) restraints added in 6.9 seconds 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 34 sheets defined 43.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.16 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 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 198 removed outlier: 3.527A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) 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 260 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 4.023A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.038A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 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 594 through 611 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.865A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 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 139 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: 4.393A 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 removed outlier: 3.808A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) 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 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 385 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 removed outlier: 3.752A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.519A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 547 removed outlier: 4.111A 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 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 596 through 608 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 650 through 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 43 through 48 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 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 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.382A 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 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 409 through 429 removed outlier: 3.780A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' 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 534 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 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 596 through 608 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.992A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' 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 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 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 426 removed outlier: 3.708A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (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 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' 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 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' 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: 6.712A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.944A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 4.035A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 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 139 Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 336 removed outlier: 4.500A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 426 removed outlier: 3.887A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 554 through 568 Processing helix chain 'E' and resid 579 through 582 No H-bonds generated for 'chain 'E' and resid 579 through 582' 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 663 removed outlier: 5.103A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.664A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 765 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 130 through 138 removed outlier: 3.717A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 225 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 294 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 Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 409 through 428 removed outlier: 4.419A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (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 505 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 613 removed outlier: 4.446A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) 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: 7.827A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.607A pdb=" N ILE A 114 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.860A 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 146 removed outlier: 3.922A 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: 4.167A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.255A 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: 6.636A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.353A 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 42 removed outlier: 7.562A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.851A pdb=" N ILE B 114 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.660A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 365 through 369 removed outlier: 3.536A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.789A 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: 8.351A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.749A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.883A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 151 through 154 Processing sheet with id= O, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.571A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.062A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= R, first strand: chain 'D' and resid 38 through 41 removed outlier: 7.155A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.584A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.981A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.208A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 641 through 645 removed outlier: 8.127A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= X, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.307A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 167 through 169 removed outlier: 5.888A pdb=" N VAL E 181 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 144 through 146 removed outlier: 3.874A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 151 through 154 Processing sheet with id= AB, first strand: chain 'E' and resid 365 through 369 removed outlier: 8.788A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 641 through 645 removed outlier: 7.996A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 8.490A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 167 through 169 removed outlier: 5.313A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 151 through 154 Processing sheet with id= AG, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.731A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 641 through 645 removed outlier: 6.342A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 540 " --> pdb=" O VAL F 573 " (cutoff:3.500A) 1267 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.23 Time building geometry restraints manager: 15.17 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: 11953 1.34 - 1.46: 6705 1.46 - 1.58: 16581 1.58 - 1.70: 43 1.70 - 1.82: 284 Bond restraints: 35566 Sorted by residual: bond pdb=" C ALA D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.332 1.387 -0.055 1.12e-02 7.97e+03 2.37e+01 bond pdb=" CG PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 1.512 1.430 0.082 2.70e-02 1.37e+03 9.30e+00 bond pdb=" CB MET C 427 " pdb=" CG MET C 427 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" CD2 PHE F 771 " pdb=" CE2 PHE F 771 " ideal model delta sigma weight residual 1.382 1.330 0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" CB PHE F 771 " pdb=" CG PHE F 771 " ideal model delta sigma weight residual 1.502 1.466 0.036 2.30e-02 1.89e+03 2.42e+00 ... (remaining 35561 not shown) Histogram of bond angle deviations from ideal: 93.04 - 102.40: 145 102.40 - 111.75: 17563 111.75 - 121.11: 21089 121.11 - 130.47: 9184 130.47 - 139.82: 110 Bond angle restraints: 48091 Sorted by residual: angle pdb=" N PRO A 170 " pdb=" CD PRO A 170 " pdb=" CG PRO A 170 " ideal model delta sigma weight residual 103.80 96.29 7.51 1.20e+00 6.94e-01 3.91e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 111.50 105.05 6.45 1.40e+00 5.10e-01 2.12e+01 angle pdb=" CA PRO B 298 " pdb=" N PRO B 298 " pdb=" CD PRO B 298 " ideal model delta sigma weight residual 112.00 105.84 6.16 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C PHE B 768 " pdb=" CA PHE B 768 " pdb=" CB PHE B 768 " ideal model delta sigma weight residual 115.79 111.16 4.63 1.19e+00 7.06e-01 1.51e+01 angle pdb=" CB PRO A 170 " pdb=" CG PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 105.40 96.55 8.85 2.30e+00 1.89e-01 1.48e+01 ... (remaining 48086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 21645 31.91 - 63.82: 483 63.82 - 95.73: 67 95.73 - 127.64: 5 127.64 - 159.55: 4 Dihedral angle restraints: 22204 sinusoidal: 9432 harmonic: 12772 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 99.56 -159.55 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 90.26 -150.26 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PA ADP F 902 " pdb=" PB ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 85.95 -145.94 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 22201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4005 0.042 - 0.084: 971 0.084 - 0.125: 380 0.125 - 0.167: 47 0.167 - 0.209: 2 Chirality restraints: 5405 Sorted by residual: chirality pdb=" CB ILE A 690 " pdb=" CA ILE A 690 " pdb=" CG1 ILE A 690 " pdb=" CG2 ILE A 690 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE D 151 " pdb=" N ILE D 151 " pdb=" C ILE D 151 " pdb=" CB ILE D 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CB THR F 679 " pdb=" CA THR F 679 " pdb=" OG1 THR F 679 " pdb=" CG2 THR F 679 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 5402 not shown) Planarity restraints: 6298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.090 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO B 298 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " -0.062 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A 170 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 454 " -0.009 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP A 454 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 454 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 454 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 454 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 454 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 454 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 454 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 454 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 454 " 0.002 2.00e-02 2.50e+03 ... (remaining 6295 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 318 2.59 - 3.17: 30157 3.17 - 3.75: 57167 3.75 - 4.32: 80079 4.32 - 4.90: 128106 Nonbonded interactions: 295827 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 903 " model vdw 2.023 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 903 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR B 525 " pdb="MG MG B 903 " model vdw 2.035 2.170 ... (remaining 295822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'B' and (resid 23 through 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 583 or resid 596 through 762)) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.870 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 94.360 Find NCS groups from input model: 3.220 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35566 Z= 0.199 Angle : 0.641 11.248 48091 Z= 0.351 Chirality : 0.043 0.209 5405 Planarity : 0.005 0.133 6298 Dihedral : 13.996 159.554 13914 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.75 % Favored : 98.20 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4391 helix: 1.08 (0.12), residues: 1946 sheet: 0.28 (0.20), residues: 659 loop : 0.35 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 454 HIS 0.008 0.001 HIS F 115 PHE 0.027 0.001 PHE A 360 TYR 0.014 0.001 TYR D 203 ARG 0.010 0.001 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 1.8687 time to fit residues: 593.3782 Evaluate side-chains 142 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.5980 chunk 334 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 133 optimal weight: 0.0020 chunk 210 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 400 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35566 Z= 0.165 Angle : 0.561 16.182 48091 Z= 0.277 Chirality : 0.042 0.162 5405 Planarity : 0.004 0.068 6298 Dihedral : 10.838 168.635 5135 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 0.67 % Allowed : 5.74 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.18 (0.13), residues: 4391 helix: 1.36 (0.12), residues: 1956 sheet: 0.34 (0.20), residues: 682 loop : 0.48 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 PHE 0.022 0.001 PHE F 771 TYR 0.022 0.002 TYR D 138 ARG 0.008 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 164 average time/residue: 1.5942 time to fit residues: 313.4071 Evaluate side-chains 142 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 333 optimal weight: 0.0470 chunk 272 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 433 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 397 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 421 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35566 Z= 0.150 Angle : 0.530 20.279 48091 Z= 0.258 Chirality : 0.042 0.152 5405 Planarity : 0.004 0.076 6298 Dihedral : 10.522 177.639 5135 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 0.91 % Allowed : 7.29 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.34 (0.13), residues: 4391 helix: 1.53 (0.12), residues: 1955 sheet: 0.32 (0.20), residues: 670 loop : 0.56 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.008 0.001 HIS F 115 PHE 0.026 0.001 PHE F 674 TYR 0.017 0.001 TYR D 138 ARG 0.005 0.000 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 MET cc_start: 0.7267 (mmm) cc_final: 0.6959 (mmt) REVERT: C 173 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.5637 (m-80) REVERT: F 46 MET cc_start: 0.2887 (mmm) cc_final: 0.2304 (mpt) REVERT: F 427 MET cc_start: 0.6052 (mmm) cc_final: 0.5668 (tpp) outliers start: 34 outliers final: 6 residues processed: 156 average time/residue: 1.6012 time to fit residues: 301.5612 Evaluate side-chains 137 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 402 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 381 optimal weight: 40.0000 chunk 114 optimal weight: 2.9990 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 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN B 458 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35566 Z= 0.332 Angle : 0.590 19.553 48091 Z= 0.289 Chirality : 0.044 0.244 5405 Planarity : 0.004 0.058 6298 Dihedral : 10.705 172.118 5135 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 0.88 % Allowed : 8.47 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.36 (0.13), residues: 4391 helix: 1.53 (0.12), residues: 1936 sheet: 0.25 (0.20), residues: 675 loop : 0.66 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 PHE 0.016 0.002 PHE A 452 TYR 0.014 0.001 TYR D 138 ARG 0.009 0.001 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6931 (mmp) REVERT: C 173 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5808 (m-80) REVERT: F 46 MET cc_start: 0.2646 (mmm) cc_final: 0.2076 (mpt) outliers start: 33 outliers final: 8 residues processed: 151 average time/residue: 1.6136 time to fit residues: 294.5242 Evaluate side-chains 139 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 317 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 363 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 217 optimal weight: 6.9990 chunk 382 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35566 Z= 0.314 Angle : 0.580 16.684 48091 Z= 0.285 Chirality : 0.044 0.159 5405 Planarity : 0.004 0.058 6298 Dihedral : 10.606 159.316 5135 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % Rotamer: Outliers : 0.94 % Allowed : 9.68 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.35 (0.13), residues: 4391 helix: 1.50 (0.12), residues: 1933 sheet: 0.26 (0.20), residues: 669 loop : 0.66 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 PHE 0.015 0.001 PHE A 452 TYR 0.022 0.001 TYR D 173 ARG 0.009 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6932 (mmp) REVERT: C 173 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: D 21 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7257 (p0) REVERT: F 46 MET cc_start: 0.2776 (mmm) cc_final: 0.2099 (mpt) outliers start: 35 outliers final: 13 residues processed: 156 average time/residue: 1.5810 time to fit residues: 296.3449 Evaluate side-chains 143 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 3.9990 chunk 383 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 426 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 458 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35566 Z= 0.387 Angle : 0.613 15.275 48091 Z= 0.301 Chirality : 0.044 0.169 5405 Planarity : 0.005 0.151 6298 Dihedral : 10.625 153.654 5135 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 1.26 % Allowed : 10.43 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.27 (0.13), residues: 4391 helix: 1.43 (0.12), residues: 1933 sheet: 0.28 (0.20), residues: 661 loop : 0.61 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 PHE 0.016 0.002 PHE A 452 TYR 0.012 0.002 TYR D 138 ARG 0.023 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 134 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5875 (m-80) REVERT: F 46 MET cc_start: 0.2624 (mmm) cc_final: 0.1883 (mpt) outliers start: 47 outliers final: 23 residues processed: 167 average time/residue: 1.4565 time to fit residues: 296.3762 Evaluate side-chains 153 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 311 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 359 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 425 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 43 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35566 Z= 0.155 Angle : 0.542 16.171 48091 Z= 0.262 Chirality : 0.042 0.181 5405 Planarity : 0.004 0.097 6298 Dihedral : 10.092 160.868 5135 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 0.80 % Allowed : 11.53 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.13), residues: 4391 helix: 1.63 (0.12), residues: 1926 sheet: 0.44 (0.21), residues: 642 loop : 0.67 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.008 0.001 HIS F 115 PHE 0.015 0.001 PHE F 771 TYR 0.014 0.001 TYR D 138 ARG 0.011 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5756 (m-80) REVERT: F 46 MET cc_start: 0.2662 (mmm) cc_final: 0.1930 (mpt) outliers start: 30 outliers final: 17 residues processed: 151 average time/residue: 1.5249 time to fit residues: 278.8240 Evaluate side-chains 145 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 128 optimal weight: 0.0570 chunk 83 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 270 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35566 Z= 0.154 Angle : 0.542 20.751 48091 Z= 0.259 Chirality : 0.042 0.202 5405 Planarity : 0.004 0.093 6298 Dihedral : 9.809 164.129 5135 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 0.78 % Allowed : 11.93 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.55 (0.13), residues: 4391 helix: 1.72 (0.12), residues: 1923 sheet: 0.47 (0.21), residues: 643 loop : 0.66 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.008 0.001 HIS F 115 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR D 138 ARG 0.006 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: F 46 MET cc_start: 0.2454 (mmm) cc_final: 0.1706 (mpt) outliers start: 29 outliers final: 16 residues processed: 151 average time/residue: 1.6021 time to fit residues: 292.8728 Evaluate side-chains 144 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 371 optimal weight: 50.0000 chunk 396 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 357 optimal weight: 0.6980 chunk 374 optimal weight: 20.0000 chunk 394 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 43 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 35566 Z= 0.502 Angle : 0.695 12.040 48091 Z= 0.342 Chirality : 0.047 0.192 5405 Planarity : 0.005 0.069 6298 Dihedral : 10.513 154.940 5135 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.05 % Allowed : 12.17 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.22 (0.13), residues: 4391 helix: 1.44 (0.12), residues: 1901 sheet: 0.26 (0.20), residues: 661 loop : 0.53 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 476 HIS 0.008 0.001 HIS F 115 PHE 0.022 0.002 PHE A 452 TYR 0.017 0.002 TYR C 755 ARG 0.011 0.001 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 MET cc_start: 0.2578 (mmm) cc_final: 0.1737 (mpt) outliers start: 39 outliers final: 20 residues processed: 160 average time/residue: 1.4334 time to fit residues: 279.3683 Evaluate side-chains 148 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 3.9990 chunk 418 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 chunk 439 optimal weight: 20.0000 chunk 404 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN D 384 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35566 Z= 0.181 Angle : 0.583 12.381 48091 Z= 0.283 Chirality : 0.042 0.144 5405 Planarity : 0.004 0.060 6298 Dihedral : 9.971 161.095 5135 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.75 % Rotamer: Outliers : 0.70 % Allowed : 12.65 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.43 (0.13), residues: 4391 helix: 1.62 (0.12), residues: 1910 sheet: 0.31 (0.21), residues: 650 loop : 0.64 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 551 HIS 0.008 0.001 HIS F 115 PHE 0.014 0.001 PHE D 139 TYR 0.012 0.001 TYR C 173 ARG 0.004 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.6186 (tmm) cc_final: 0.5945 (ptm) REVERT: F 46 MET cc_start: 0.2270 (mmm) cc_final: 0.1476 (mpt) outliers start: 26 outliers final: 17 residues processed: 155 average time/residue: 1.4361 time to fit residues: 271.4647 Evaluate side-chains 146 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 51 optimal weight: 0.0050 chunk 97 optimal weight: 0.0060 chunk 350 optimal weight: 1.9990 chunk 146 optimal weight: 0.0570 chunk 359 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.099294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062351 restraints weight = 107406.022| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.88 r_work: 0.2880 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 35566 Z= 0.146 Angle : 0.561 12.402 48091 Z= 0.270 Chirality : 0.042 0.186 5405 Planarity : 0.004 0.059 6298 Dihedral : 9.528 167.394 5135 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 0.70 % Allowed : 12.76 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.13), residues: 4391 helix: 1.76 (0.12), residues: 1914 sheet: 0.35 (0.21), residues: 651 loop : 0.65 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 551 HIS 0.008 0.001 HIS F 115 PHE 0.016 0.001 PHE D 139 TYR 0.010 0.001 TYR D 143 ARG 0.007 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8191.47 seconds wall clock time: 148 minutes 56.09 seconds (8936.09 seconds total)