Starting phenix.real_space_refine on Thu Feb 22 23:05:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmy_23442/02_2024/7lmy_23442_updated.pdb" } resolution = 2.4 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 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 22338 2.51 5 N 6300 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 120": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 700": "NH1" <-> "NH2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E ARG 700": "NH1" <-> "NH2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F ARG 700": "NH1" <-> "NH2" Residue "F GLU 730": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35646 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "B" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "C" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "D" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "E" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "F" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 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: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 19.78, per 1000 atoms: 0.55 Number of scatterers: 35646 At special positions: 0 Unit cell: (175.395, 169.017, 113.741, 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 192 16.00 P 36 15.00 Mg 12 11.99 O 6768 8.00 N 6300 7.00 C 22338 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: 14.44 Conformation dependent library (CDL) restraints added in 7.2 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 30 sheets defined 43.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 130 through 138 removed outlier: 4.596A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 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 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 429 removed outlier: 3.512A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (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 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.514A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 613 removed outlier: 4.822A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.191A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.596A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 275 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 334 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 429 removed outlier: 3.512A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.515A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 613 removed outlier: 4.822A pdb=" N THR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.190A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 138 removed outlier: 4.596A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 275 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 334 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 429 removed outlier: 3.512A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 483 through 498 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 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.514A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 613 removed outlier: 4.823A pdb=" N THR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 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: 4.190A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.596A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 275 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 334 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 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 429 removed outlier: 3.512A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (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 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 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.515A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 613 removed outlier: 4.823A pdb=" N THR D 613 " --> pdb=" O ASP D 609 " (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 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.190A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'E' and resid 43 through 49 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 138 removed outlier: 4.596A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 275 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 334 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 408 through 429 removed outlier: 3.511A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.514A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 613 removed outlier: 4.823A pdb=" N THR E 613 " --> pdb=" O ASP E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.190A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 130 through 138 removed outlier: 4.595A 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 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' 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 232 Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 429 removed outlier: 3.512A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.514A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 613 removed outlier: 4.822A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 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 removed outlier: 4.190A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.478A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.742A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.670A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.436A 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: 8.930A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.478A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.743A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.669A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 8.931A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.478A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.742A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.669A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.931A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.479A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.742A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.670A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 8.931A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.479A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.742A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.669A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.931A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 84 removed outlier: 7.478A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.743A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.669A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 8.930A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3582 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: 14.62 Time building geometry restraints manager: 15.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12156 1.35 - 1.47: 7157 1.47 - 1.59: 16602 1.59 - 1.71: 37 1.71 - 1.83: 300 Bond restraints: 36252 Sorted by residual: bond pdb=" C10 Y6Y A 903 " pdb=" S Y6Y A 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C10 Y6Y B 903 " pdb=" S Y6Y B 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C10 Y6Y F 903 " pdb=" S Y6Y F 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C10 Y6Y D 903 " pdb=" S Y6Y D 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C10 Y6Y E 903 " pdb=" S Y6Y E 903 " ideal model delta sigma weight residual 1.774 1.595 0.179 2.00e-02 2.50e+03 8.04e+01 ... (remaining 36247 not shown) Histogram of bond angle deviations from ideal: 99.93 - 107.95: 1629 107.95 - 115.97: 22506 115.97 - 124.00: 23996 124.00 - 132.02: 847 132.02 - 140.04: 54 Bond angle restraints: 49032 Sorted by residual: angle pdb=" CB ARG C 225 " pdb=" CG ARG C 225 " pdb=" CD ARG C 225 " ideal model delta sigma weight residual 111.30 126.26 -14.96 2.30e+00 1.89e-01 4.23e+01 angle pdb=" CB ARG B 225 " pdb=" CG ARG B 225 " pdb=" CD ARG B 225 " ideal model delta sigma weight residual 111.30 126.24 -14.94 2.30e+00 1.89e-01 4.22e+01 angle pdb=" CB ARG D 225 " pdb=" CG ARG D 225 " pdb=" CD ARG D 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG E 225 " pdb=" CG ARG E 225 " pdb=" CD ARG E 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG F 225 " pdb=" CG ARG F 225 " pdb=" CD ARG F 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 ... (remaining 49027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20575 17.86 - 35.72: 1602 35.72 - 53.57: 365 53.57 - 71.43: 150 71.43 - 89.29: 72 Dihedral angle restraints: 22764 sinusoidal: 9882 harmonic: 12882 Sorted by residual: dihedral pdb=" CA GLN C 19 " pdb=" C GLN C 19 " pdb=" N LYS C 20 " pdb=" CA LYS C 20 " ideal model delta harmonic sigma weight residual 180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN A 19 " pdb=" C GLN A 19 " pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN B 19 " pdb=" C GLN B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 22761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4407 0.053 - 0.106: 887 0.106 - 0.158: 172 0.158 - 0.211: 6 0.211 - 0.264: 6 Chirality restraints: 5478 Sorted by residual: chirality pdb=" C17 Y6Y A 903 " pdb=" C18 Y6Y A 903 " pdb=" C21 Y6Y A 903 " pdb=" S1 Y6Y A 903 " both_signs ideal model delta sigma weight residual False 3.51 3.24 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C17 Y6Y F 903 " pdb=" C18 Y6Y F 903 " pdb=" C21 Y6Y F 903 " pdb=" S1 Y6Y F 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C17 Y6Y B 903 " pdb=" C18 Y6Y B 903 " pdb=" C21 Y6Y B 903 " pdb=" S1 Y6Y B 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5475 not shown) Planarity restraints: 6390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 237 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO D 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 237 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 238 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 237 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.88e+01 pdb=" N PRO C 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.058 5.00e-02 4.00e+02 ... (remaining 6387 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 294 2.57 - 3.15: 28789 3.15 - 3.73: 57150 3.73 - 4.32: 82618 4.32 - 4.90: 130990 Nonbonded interactions: 299841 Sorted by model distance: nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 904 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 904 " model vdw 1.996 2.170 nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 904 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 904 " model vdw 2.011 2.170 ... (remaining 299836 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.190 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 95.900 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.005 0.180 36252 Z= 0.318 Angle : 0.769 16.598 49032 Z= 0.395 Chirality : 0.045 0.264 5478 Planarity : 0.005 0.109 6390 Dihedral : 15.350 89.289 14400 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.89 % Allowed : 0.47 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.96 (0.13), residues: 4434 helix: 0.96 (0.12), residues: 1962 sheet: 0.52 (0.20), residues: 654 loop : 0.53 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.004 0.001 HIS A 183 PHE 0.018 0.001 PHE C 742 TYR 0.011 0.001 TYR C 203 ARG 0.010 0.001 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 427 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6588 (mmm) outliers start: 72 outliers final: 5 residues processed: 283 average time/residue: 2.2190 time to fit residues: 712.3029 Evaluate side-chains 150 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain F residue 427 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 115 HIS C 115 HIS D 115 HIS D 226 HIS E 115 HIS F 115 HIS F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 36252 Z= 0.300 Angle : 0.555 6.135 49032 Z= 0.288 Chirality : 0.044 0.145 5478 Planarity : 0.005 0.080 6390 Dihedral : 11.207 80.000 5466 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 6.05 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4434 helix: 1.18 (0.12), residues: 1986 sheet: 0.59 (0.20), residues: 654 loop : 0.69 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.008 0.001 HIS E 115 PHE 0.011 0.001 PHE B 563 TYR 0.007 0.001 TYR E 203 ARG 0.009 0.001 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 4.208 Fit side-chains revert: symmetry clash REVERT: E 336 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6169 (mtmm) outliers start: 42 outliers final: 9 residues processed: 156 average time/residue: 1.6758 time to fit residues: 313.7891 Evaluate side-chains 140 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 335 optimal weight: 5.9990 chunk 274 optimal weight: 0.0070 chunk 111 optimal weight: 6.9990 chunk 403 optimal weight: 0.6980 chunk 436 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 400 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36252 Z= 0.172 Angle : 0.485 7.136 49032 Z= 0.251 Chirality : 0.042 0.147 5478 Planarity : 0.004 0.067 6390 Dihedral : 10.826 79.777 5448 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.05 % Allowed : 6.83 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.13), residues: 4434 helix: 1.39 (0.12), residues: 1986 sheet: 0.69 (0.20), residues: 636 loop : 0.82 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 454 HIS 0.018 0.002 HIS F 115 PHE 0.011 0.001 PHE B 131 TYR 0.006 0.001 TYR F 244 ARG 0.008 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 4.114 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 154 average time/residue: 1.4980 time to fit residues: 281.5143 Evaluate side-chains 143 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 0.7980 chunk 429 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 384 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 36252 Z= 0.270 Angle : 0.495 8.623 49032 Z= 0.255 Chirality : 0.043 0.148 5478 Planarity : 0.004 0.061 6390 Dihedral : 10.783 80.368 5448 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.45 % Allowed : 7.62 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.13), residues: 4434 helix: 1.44 (0.12), residues: 1974 sheet: 0.70 (0.20), residues: 636 loop : 0.80 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.012 0.001 HIS A 183 PHE 0.012 0.001 PHE B 131 TYR 0.006 0.001 TYR E 755 ARG 0.005 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 4.276 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 1.5392 time to fit residues: 267.8387 Evaluate side-chains 140 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.0570 chunk 243 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 385 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 226 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN D 115 HIS E 115 HIS E 226 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN F 115 HIS F 494 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 36252 Z= 0.398 Angle : 0.543 9.647 49032 Z= 0.280 Chirality : 0.045 0.150 5478 Planarity : 0.004 0.061 6390 Dihedral : 10.794 80.557 5448 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.84 % Allowed : 7.89 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.42 (0.13), residues: 4434 helix: 1.37 (0.12), residues: 1980 sheet: 0.39 (0.20), residues: 678 loop : 0.91 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.012 0.002 HIS E 115 PHE 0.012 0.002 PHE E 563 TYR 0.010 0.001 TYR B 755 ARG 0.005 0.000 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 4.429 Fit side-chains REVERT: B 336 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6189 (mtmm) outliers start: 32 outliers final: 14 residues processed: 156 average time/residue: 1.6440 time to fit residues: 308.9631 Evaluate side-chains 145 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 5.9990 chunk 386 optimal weight: 7.9990 chunk 84 optimal weight: 50.0000 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 429 optimal weight: 0.6980 chunk 356 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 225 optimal weight: 0.0010 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 183 HIS E 115 HIS E 183 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36252 Z= 0.151 Angle : 0.469 8.924 49032 Z= 0.243 Chirality : 0.042 0.147 5478 Planarity : 0.004 0.055 6390 Dihedral : 10.321 84.096 5448 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.13), residues: 4434 helix: 1.54 (0.12), residues: 1980 sheet: 0.39 (0.20), residues: 678 loop : 0.94 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.011 0.001 HIS A 115 PHE 0.012 0.001 PHE B 363 TYR 0.021 0.001 TYR E 173 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 4.427 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 1.5612 time to fit residues: 273.2874 Evaluate side-chains 140 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 244 optimal weight: 3.9990 chunk 313 optimal weight: 30.0000 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 10.0000 chunk 239 optimal weight: 30.0000 chunk 427 optimal weight: 8.9990 chunk 267 optimal weight: 0.3980 chunk 260 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36252 Z= 0.212 Angle : 0.473 9.282 49032 Z= 0.242 Chirality : 0.042 0.149 5478 Planarity : 0.004 0.053 6390 Dihedral : 10.161 85.049 5448 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.66 % Allowed : 8.54 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.58 (0.13), residues: 4434 helix: 1.58 (0.12), residues: 1980 sheet: 0.43 (0.20), residues: 678 loop : 0.90 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.010 0.001 HIS A 115 PHE 0.010 0.001 PHE B 131 TYR 0.017 0.001 TYR E 173 ARG 0.005 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 4.231 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 1.5359 time to fit residues: 270.8022 Evaluate side-chains 143 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 36252 Z= 0.249 Angle : 0.484 9.570 49032 Z= 0.246 Chirality : 0.043 0.148 5478 Planarity : 0.004 0.053 6390 Dihedral : 10.022 86.224 5448 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.97 % Allowed : 8.23 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.13), residues: 4434 helix: 1.55 (0.12), residues: 1980 sheet: 0.46 (0.20), residues: 678 loop : 0.91 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.012 0.001 HIS B 115 PHE 0.009 0.001 PHE F 302 TYR 0.018 0.001 TYR E 173 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 3.883 Fit side-chains REVERT: B 508 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7120 (ttm) outliers start: 37 outliers final: 22 residues processed: 151 average time/residue: 1.4804 time to fit residues: 271.5855 Evaluate side-chains 148 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 3.9990 chunk 409 optimal weight: 6.9990 chunk 374 optimal weight: 0.0870 chunk 398 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 397 optimal weight: 3.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 36252 Z= 0.272 Angle : 0.502 10.571 49032 Z= 0.253 Chirality : 0.043 0.144 5478 Planarity : 0.004 0.052 6390 Dihedral : 9.945 86.693 5448 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.79 % Allowed : 8.41 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.13), residues: 4434 helix: 1.58 (0.12), residues: 1980 sheet: 0.47 (0.20), residues: 678 loop : 0.90 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.018 0.002 HIS C 115 PHE 0.009 0.001 PHE F 302 TYR 0.018 0.001 TYR E 173 ARG 0.005 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 4.282 Fit side-chains REVERT: B 508 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7163 (ttm) outliers start: 30 outliers final: 22 residues processed: 145 average time/residue: 1.5379 time to fit residues: 271.9031 Evaluate side-chains 146 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 6.9990 chunk 421 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 442 optimal weight: 1.9990 chunk 407 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36252 Z= 0.162 Angle : 0.478 10.749 49032 Z= 0.241 Chirality : 0.042 0.148 5478 Planarity : 0.004 0.051 6390 Dihedral : 9.725 88.184 5448 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.58 % Allowed : 8.62 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4434 helix: 1.62 (0.12), residues: 1992 sheet: 0.44 (0.21), residues: 660 loop : 0.95 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.023 0.002 HIS F 115 PHE 0.009 0.001 PHE E 363 TYR 0.018 0.001 TYR E 173 ARG 0.005 0.000 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 4.057 Fit side-chains REVERT: B 508 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7130 (ttm) outliers start: 22 outliers final: 19 residues processed: 141 average time/residue: 1.5552 time to fit residues: 266.4543 Evaluate side-chains 144 residues out of total 3822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** 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 = 0.3759 r_free = 0.3759 target = 0.096477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056313 restraints weight = 76392.899| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.73 r_work: 0.2724 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36252 Z= 0.291 Angle : 0.510 11.411 49032 Z= 0.255 Chirality : 0.043 0.143 5478 Planarity : 0.004 0.052 6390 Dihedral : 9.727 87.564 5448 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.60 % Allowed : 8.70 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.13), residues: 4434 helix: 1.58 (0.12), residues: 1992 sheet: 0.44 (0.21), residues: 660 loop : 0.93 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.025 0.002 HIS E 115 PHE 0.009 0.001 PHE F 302 TYR 0.018 0.001 TYR E 173 ARG 0.005 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8390.89 seconds wall clock time: 152 minutes 16.64 seconds (9136.64 seconds total)