Starting phenix.real_space_refine on Thu Feb 22 17:45:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rla_24523/02_2024/7rla_24523_updated.pdb" } resolution = 3.1 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= 0.022 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 21876 2.51 5 N 6132 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 34944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5760 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 16.95, per 1000 atoms: 0.49 Number of scatterers: 34944 At special positions: 0 Unit cell: (180.728, 184.034, 123.424, 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 6696 8.00 N 6132 7.00 C 21876 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: 14.32 Conformation dependent library (CDL) restraints added in 7.3 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 12 sheets defined 35.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.549A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.966A pdb=" N ALA A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.664A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.536A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.985A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.808A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.825A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 4.078A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.610A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.648A pdb=" N ASP A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.502A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.519A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 660 removed outlier: 4.326A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.533A pdb=" N ALA A 739 " --> pdb=" O HIS A 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.549A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.966A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.664A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.535A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.985A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.806A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.825A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 4.078A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.611A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.648A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.503A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.518A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 660 removed outlier: 4.326A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 675 No H-bonds generated for 'chain 'B' and resid 672 through 675' Processing helix chain 'B' and resid 684 through 704 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.533A pdb=" N ALA B 739 " --> pdb=" O HIS B 735 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.549A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.966A pdb=" N ALA C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.664A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.535A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) 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 333 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.985A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.807A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.826A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.078A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.610A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 removed outlier: 3.649A pdb=" N ASP C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 565 " --> pdb=" O GLU C 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 567 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.502A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.518A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 660 removed outlier: 4.327A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 675 No H-bonds generated for 'chain 'C' and resid 672 through 675' Processing helix chain 'C' and resid 684 through 704 Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.533A pdb=" N ALA C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.550A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.968A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.665A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.534A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.986A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.808A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.825A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 removed outlier: 4.078A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.611A pdb=" N LEU D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 removed outlier: 3.648A pdb=" N ASP D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS D 565 " --> pdb=" O GLU D 561 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.502A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 removed outlier: 3.520A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 660 removed outlier: 4.326A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 675 No H-bonds generated for 'chain 'D' and resid 672 through 675' Processing helix chain 'D' and resid 684 through 704 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.533A pdb=" N ALA D 739 " --> pdb=" O HIS D 735 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 192 through 198 removed outlier: 3.550A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.967A pdb=" N ALA E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.666A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 294 removed outlier: 3.535A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 374 through 386 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.985A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.808A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.826A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 4.079A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 551 removed outlier: 3.610A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 568 removed outlier: 3.648A pdb=" N ASP E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS E 565 " --> pdb=" O GLU E 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG E 567 " --> pdb=" O PHE E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 585 removed outlier: 3.502A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 removed outlier: 3.519A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 660 removed outlier: 4.326A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 675 No H-bonds generated for 'chain 'E' and resid 672 through 675' Processing helix chain 'E' and resid 684 through 704 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.534A pdb=" N ALA E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 192 through 198 removed outlier: 3.550A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.966A pdb=" N ALA F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 260 removed outlier: 3.664A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 294 removed outlier: 3.536A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) 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 333 Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.985A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.604A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.808A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.825A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 4.079A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 551 removed outlier: 3.610A pdb=" N LEU F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 removed outlier: 3.648A pdb=" N ASP F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS F 565 " --> pdb=" O GLU F 561 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.502A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 removed outlier: 3.518A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 660 removed outlier: 4.327A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 675 No H-bonds generated for 'chain 'F' and resid 672 through 675' Processing helix chain 'F' and resid 684 through 704 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.533A pdb=" N ALA F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.644A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.644A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY C 245 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 347 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.645A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.645A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.644A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 369 removed outlier: 8.475A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY F 245 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR F 347 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.644A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2430 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: 10.62 Time building geometry restraints manager: 15.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 12083 1.37 - 1.52: 9425 1.52 - 1.66: 13706 1.66 - 1.80: 198 1.80 - 1.95: 102 Bond restraints: 35514 Sorted by residual: bond pdb=" C ASP F 169 " pdb=" N PRO F 170 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.23e-02 6.61e+03 9.31e+00 bond pdb=" C ASP E 169 " pdb=" N PRO E 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 9.15e+00 bond pdb=" C ASP C 169 " pdb=" N PRO C 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 9.07e+00 bond pdb=" C ASP D 169 " pdb=" N PRO D 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" C ASP A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.23e-02 6.61e+03 8.83e+00 ... (remaining 35509 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 1235 106.87 - 113.65: 19638 113.65 - 120.42: 13536 120.42 - 127.20: 13282 127.20 - 133.97: 351 Bond angle restraints: 48042 Sorted by residual: angle pdb=" N GLU E 470 " pdb=" CA GLU E 470 " pdb=" C GLU E 470 " ideal model delta sigma weight residual 109.81 121.06 -11.25 1.53e+00 4.27e-01 5.40e+01 angle pdb=" N GLU B 470 " pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 109.81 121.05 -11.24 1.53e+00 4.27e-01 5.40e+01 angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 109.81 121.04 -11.23 1.53e+00 4.27e-01 5.39e+01 angle pdb=" N GLU D 470 " pdb=" CA GLU D 470 " pdb=" C GLU D 470 " ideal model delta sigma weight residual 109.81 121.02 -11.21 1.53e+00 4.27e-01 5.37e+01 angle pdb=" N GLU F 470 " pdb=" CA GLU F 470 " pdb=" C GLU F 470 " ideal model delta sigma weight residual 109.81 121.01 -11.20 1.53e+00 4.27e-01 5.36e+01 ... (remaining 48037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 19354 15.59 - 31.19: 1982 31.19 - 46.78: 576 46.78 - 62.38: 102 62.38 - 77.97: 42 Dihedral angle restraints: 22056 sinusoidal: 9336 harmonic: 12720 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N VAL A 471 " pdb=" CA VAL A 471 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N VAL B 471 " pdb=" CA VAL B 471 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU E 470 " pdb=" C GLU E 470 " pdb=" N VAL E 471 " pdb=" CA VAL E 471 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 22053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4170 0.050 - 0.100: 1018 0.100 - 0.150: 218 0.150 - 0.200: 12 0.200 - 0.250: 18 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CA GLU D 470 " pdb=" N GLU D 470 " pdb=" C GLU D 470 " pdb=" CB GLU D 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLU A 470 " pdb=" N GLU A 470 " pdb=" C GLU A 470 " pdb=" CB GLU A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLU E 470 " pdb=" N GLU E 470 " pdb=" C GLU E 470 " pdb=" CB GLU E 470 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 517 " 0.021 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR D 517 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR D 517 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 517 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 517 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR D 517 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 517 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR D 517 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 517 " -0.021 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR F 517 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR F 517 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR F 517 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR F 517 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 517 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 517 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR F 517 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " -0.021 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 517 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " 0.003 2.00e-02 2.50e+03 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 366 2.61 - 3.18: 29320 3.18 - 3.75: 51787 3.75 - 4.33: 67257 4.33 - 4.90: 108645 Nonbonded interactions: 257375 Sorted by model distance: nonbonded pdb=" O ARG A 745 " pdb=" NE2 GLN F 763 " model vdw 2.035 2.520 nonbonded pdb=" O1A AGS F 902 " pdb="MG MG F 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS E 902 " pdb="MG MG E 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS D 902 " pdb="MG MG D 903 " model vdw 2.088 2.170 nonbonded pdb=" O1A AGS C 902 " pdb="MG MG C 903 " model vdw 2.088 2.170 ... (remaining 257370 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: 0.830 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: 5.820 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 87.270 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.270 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35514 Z= 0.208 Angle : 0.778 14.758 48042 Z= 0.435 Chirality : 0.047 0.250 5436 Planarity : 0.004 0.046 6288 Dihedral : 13.994 77.971 13812 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4398 helix: 0.22 (0.14), residues: 1458 sheet: 0.27 (0.26), residues: 402 loop : -2.35 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 454 HIS 0.001 0.000 HIS D 384 PHE 0.026 0.002 PHE C 758 TYR 0.059 0.004 TYR F 517 ARG 0.005 0.000 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8825 (m-80) cc_final: 0.8568 (m-80) REVERT: A 338 ARG cc_start: 0.7973 (pmt-80) cc_final: 0.6880 (pmt-80) REVERT: A 562 ILE cc_start: 0.6636 (mt) cc_final: 0.6178 (mt) REVERT: A 678 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7879 (pmm) REVERT: B 203 TYR cc_start: 0.8835 (m-80) cc_final: 0.8140 (m-80) REVERT: C 203 TYR cc_start: 0.8449 (m-80) cc_final: 0.7275 (m-80) REVERT: C 217 LYS cc_start: 0.9429 (mttt) cc_final: 0.9142 (mmtm) REVERT: C 276 SER cc_start: 0.8673 (p) cc_final: 0.8322 (p) REVERT: C 509 THR cc_start: 0.9324 (m) cc_final: 0.9117 (m) REVERT: E 205 ASP cc_start: 0.8642 (m-30) cc_final: 0.8231 (m-30) REVERT: E 217 LYS cc_start: 0.9504 (mttt) cc_final: 0.9230 (mttp) REVERT: F 562 ILE cc_start: 0.6917 (mt) cc_final: 0.6437 (mt) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.4700 time to fit residues: 284.9949 Evaluate side-chains 259 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN F 296 ASN F 602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 35514 Z= 0.473 Angle : 0.735 12.629 48042 Z= 0.362 Chirality : 0.049 0.168 5436 Planarity : 0.005 0.050 6288 Dihedral : 7.883 59.188 5025 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.20 % Allowed : 8.68 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.45 (0.12), residues: 4398 helix: 0.33 (0.13), residues: 1572 sheet: 0.72 (0.27), residues: 402 loop : -2.27 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP F 551 HIS 0.007 0.001 HIS C 406 PHE 0.022 0.002 PHE D 506 TYR 0.028 0.002 TYR B 203 ARG 0.008 0.001 ARG C 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 4.198 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: -0.0411 (tpp) cc_final: -0.0652 (tpp) REVERT: A 332 MET cc_start: 0.9353 (mtp) cc_final: 0.9040 (mtp) REVERT: A 678 MET cc_start: 0.8318 (pmm) cc_final: 0.8090 (pmm) REVERT: A 757 MET cc_start: 0.8980 (tmm) cc_final: 0.8661 (tmm) REVERT: B 84 MET cc_start: -0.0150 (tpp) cc_final: -0.0465 (tpp) REVERT: B 454 TRP cc_start: 0.9342 (t-100) cc_final: 0.8733 (t-100) REVERT: B 470 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: B 689 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 84 MET cc_start: -0.1079 (tpp) cc_final: -0.1297 (tpp) REVERT: C 203 TYR cc_start: 0.9168 (m-80) cc_final: 0.8383 (m-80) REVERT: C 315 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8668 (pttp) REVERT: C 580 ASP cc_start: 0.9016 (p0) cc_final: 0.8792 (p0) REVERT: C 678 MET cc_start: 0.8089 (pmm) cc_final: 0.7765 (pmm) REVERT: D 203 TYR cc_start: 0.9171 (m-10) cc_final: 0.8943 (m-80) REVERT: D 470 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: D 678 MET cc_start: 0.8104 (pmm) cc_final: 0.7849 (pmm) REVERT: D 689 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8415 (tm-30) REVERT: E 203 TYR cc_start: 0.9291 (m-10) cc_final: 0.8630 (m-80) REVERT: E 449 MET cc_start: 0.9062 (tpp) cc_final: 0.8740 (tpp) REVERT: E 550 MET cc_start: 0.7127 (ppp) cc_final: 0.6864 (ppp) REVERT: E 678 MET cc_start: 0.8046 (pmm) cc_final: 0.7834 (pmm) REVERT: E 689 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8328 (tm-30) REVERT: F 442 MET cc_start: 0.9398 (mpp) cc_final: 0.9178 (pmm) REVERT: F 757 MET cc_start: 0.8969 (tmm) cc_final: 0.8743 (tmm) outliers start: 45 outliers final: 27 residues processed: 279 average time/residue: 0.4203 time to fit residues: 202.7357 Evaluate side-chains 254 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 398 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 354 optimal weight: 0.5980 chunk 395 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 103 GLN A 296 ASN D 21 ASN D 296 ASN F 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35514 Z= 0.160 Angle : 0.509 7.909 48042 Z= 0.247 Chirality : 0.043 0.150 5436 Planarity : 0.003 0.053 6288 Dihedral : 7.346 58.655 5022 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.30 % Allowed : 10.76 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.12 (0.13), residues: 4398 helix: 0.81 (0.14), residues: 1572 sheet: 0.97 (0.27), residues: 372 loop : -2.20 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 551 HIS 0.003 0.000 HIS C 406 PHE 0.012 0.001 PHE C 618 TYR 0.017 0.002 TYR C 203 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 233 time to evaluate : 4.218 Fit side-chains REVERT: A 84 MET cc_start: -0.0352 (tpp) cc_final: -0.0583 (tpp) REVERT: A 466 GLU cc_start: 0.8579 (mp0) cc_final: 0.8379 (mp0) REVERT: A 546 GLU cc_start: 0.8746 (tt0) cc_final: 0.8202 (mt-10) REVERT: B 84 MET cc_start: -0.0261 (tpp) cc_final: -0.0611 (tpp) REVERT: B 449 MET cc_start: 0.9083 (tpp) cc_final: 0.8662 (tpp) REVERT: B 454 TRP cc_start: 0.9285 (t-100) cc_final: 0.8655 (t-100) REVERT: B 689 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 169 ASP cc_start: 0.1100 (OUTLIER) cc_final: 0.0809 (p0) REVERT: C 203 TYR cc_start: 0.9357 (m-80) cc_final: 0.9115 (m-80) REVERT: C 315 LYS cc_start: 0.9035 (ptpp) cc_final: 0.8682 (pttp) REVERT: C 678 MET cc_start: 0.7940 (pmm) cc_final: 0.7661 (pmm) REVERT: D 169 ASP cc_start: 0.1276 (OUTLIER) cc_final: 0.1032 (p0) REVERT: D 203 TYR cc_start: 0.9165 (m-10) cc_final: 0.8955 (m-80) REVERT: D 315 LYS cc_start: 0.8985 (ptpp) cc_final: 0.8737 (pttp) REVERT: D 689 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 203 TYR cc_start: 0.9398 (m-10) cc_final: 0.8743 (m-80) REVERT: E 315 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8783 (pttp) REVERT: E 449 MET cc_start: 0.9073 (tpp) cc_final: 0.8795 (tpp) REVERT: E 689 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8259 (tm-30) REVERT: F 315 LYS cc_start: 0.8995 (ptpp) cc_final: 0.8781 (pttm) REVERT: F 449 MET cc_start: 0.9072 (tpp) cc_final: 0.8815 (tpp) REVERT: F 757 MET cc_start: 0.8897 (tmm) cc_final: 0.8577 (tmm) outliers start: 49 outliers final: 32 residues processed: 273 average time/residue: 0.4188 time to fit residues: 198.2722 Evaluate side-chains 253 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 7.9990 chunk 299 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 399 optimal weight: 8.9990 chunk 423 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 379 optimal weight: 50.0000 chunk 114 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN B 21 ASN B 296 ASN C 21 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35514 Z= 0.291 Angle : 0.551 10.266 48042 Z= 0.264 Chirality : 0.044 0.153 5436 Planarity : 0.003 0.051 6288 Dihedral : 7.384 59.937 5022 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.00 % Allowed : 11.63 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.78 (0.13), residues: 4398 helix: 1.07 (0.14), residues: 1608 sheet: 1.11 (0.27), residues: 372 loop : -2.03 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 551 HIS 0.002 0.001 HIS C 406 PHE 0.010 0.001 PHE C 618 TYR 0.020 0.001 TYR E 203 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 211 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.0343 (tpp) cc_final: -0.0589 (tpp) REVERT: A 315 LYS cc_start: 0.9028 (pttm) cc_final: 0.8814 (pttp) REVERT: A 332 MET cc_start: 0.9334 (mtp) cc_final: 0.8968 (mtp) REVERT: A 402 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: A 449 MET cc_start: 0.9233 (mmm) cc_final: 0.8794 (tpp) REVERT: A 466 GLU cc_start: 0.8742 (mp0) cc_final: 0.8448 (mp0) REVERT: A 546 GLU cc_start: 0.8755 (tt0) cc_final: 0.8517 (mt-10) REVERT: B 84 MET cc_start: -0.0249 (tpp) cc_final: -0.0587 (tpp) REVERT: B 217 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.9350 (mmtm) REVERT: B 449 MET cc_start: 0.9145 (tpp) cc_final: 0.8764 (tpp) REVERT: B 454 TRP cc_start: 0.9324 (t-100) cc_final: 0.8657 (t-100) REVERT: B 689 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 169 ASP cc_start: 0.1254 (OUTLIER) cc_final: 0.0916 (p0) REVERT: C 315 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8837 (pttm) REVERT: C 678 MET cc_start: 0.7994 (pmm) cc_final: 0.7761 (pmm) REVERT: D 169 ASP cc_start: 0.1052 (OUTLIER) cc_final: 0.0748 (p0) REVERT: D 203 TYR cc_start: 0.9238 (m-10) cc_final: 0.8968 (m-80) REVERT: D 315 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8703 (pttp) REVERT: D 689 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8332 (tm-30) REVERT: E 203 TYR cc_start: 0.9186 (m-10) cc_final: 0.8908 (m-80) REVERT: E 315 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8749 (pttp) REVERT: E 449 MET cc_start: 0.9153 (tpp) cc_final: 0.8689 (tpp) REVERT: E 689 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8245 (tm-30) REVERT: F 551 TRP cc_start: 0.7862 (t-100) cc_final: 0.7598 (t-100) outliers start: 75 outliers final: 50 residues processed: 268 average time/residue: 0.4039 time to fit residues: 187.2186 Evaluate side-chains 258 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 204 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 315 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 361 optimal weight: 0.0980 chunk 292 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 216 optimal weight: 0.6980 chunk 380 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35514 Z= 0.165 Angle : 0.503 8.634 48042 Z= 0.237 Chirality : 0.043 0.163 5436 Planarity : 0.003 0.054 6288 Dihedral : 7.152 59.117 5022 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.78 % Allowed : 12.49 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.62 (0.13), residues: 4398 helix: 1.22 (0.14), residues: 1602 sheet: 1.16 (0.27), residues: 372 loop : -1.93 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 551 HIS 0.002 0.000 HIS D 406 PHE 0.008 0.001 PHE C 618 TYR 0.018 0.001 TYR C 203 ARG 0.005 0.000 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 223 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.0347 (tpp) cc_final: -0.0637 (tpp) REVERT: A 315 LYS cc_start: 0.9031 (pttm) cc_final: 0.8811 (pttp) REVERT: A 332 MET cc_start: 0.9298 (mtp) cc_final: 0.8910 (mtp) REVERT: A 449 MET cc_start: 0.9217 (mmm) cc_final: 0.8751 (tpp) REVERT: A 466 GLU cc_start: 0.8692 (mp0) cc_final: 0.8396 (mp0) REVERT: A 546 GLU cc_start: 0.8752 (tt0) cc_final: 0.8509 (mt-10) REVERT: B 84 MET cc_start: -0.0252 (tpp) cc_final: -0.0630 (tpp) REVERT: B 217 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.9326 (mmtm) REVERT: B 449 MET cc_start: 0.9173 (tpp) cc_final: 0.8787 (tpp) REVERT: B 454 TRP cc_start: 0.9310 (t-100) cc_final: 0.8622 (t-100) REVERT: B 464 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9378 (mm) REVERT: B 689 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 169 ASP cc_start: 0.1227 (OUTLIER) cc_final: 0.0877 (p0) REVERT: C 678 MET cc_start: 0.8003 (pmm) cc_final: 0.7754 (pmm) REVERT: D 84 MET cc_start: -0.0903 (tpp) cc_final: -0.1109 (tpp) REVERT: D 169 ASP cc_start: 0.1034 (OUTLIER) cc_final: 0.0722 (p0) REVERT: D 203 TYR cc_start: 0.9231 (m-10) cc_final: 0.8973 (m-80) REVERT: D 315 LYS cc_start: 0.9015 (ptpp) cc_final: 0.8698 (pttp) REVERT: D 466 GLU cc_start: 0.8797 (mp0) cc_final: 0.8421 (mp0) REVERT: D 689 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8304 (tm-30) REVERT: E 203 TYR cc_start: 0.9150 (m-10) cc_final: 0.8829 (m-80) REVERT: E 315 LYS cc_start: 0.9011 (ptpp) cc_final: 0.8746 (pttp) REVERT: E 464 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9399 (mm) REVERT: E 466 GLU cc_start: 0.8846 (mp0) cc_final: 0.8580 (mp0) REVERT: E 549 THR cc_start: 0.8347 (t) cc_final: 0.8061 (p) REVERT: E 689 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 315 LYS cc_start: 0.9010 (ptpp) cc_final: 0.8784 (pttp) outliers start: 67 outliers final: 47 residues processed: 280 average time/residue: 0.4250 time to fit residues: 204.6131 Evaluate side-chains 258 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 0.7980 chunk 381 optimal weight: 0.0870 chunk 83 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 423 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 140 optimal weight: 0.4980 chunk 222 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 337 GLN F 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35514 Z= 0.142 Angle : 0.502 11.177 48042 Z= 0.233 Chirality : 0.042 0.150 5436 Planarity : 0.003 0.051 6288 Dihedral : 6.900 59.285 5022 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.62 % Allowed : 13.02 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.49 (0.13), residues: 4398 helix: 1.36 (0.14), residues: 1602 sheet: 1.17 (0.27), residues: 372 loop : -1.86 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 551 HIS 0.002 0.000 HIS C 317 PHE 0.006 0.001 PHE C 618 TYR 0.013 0.001 TYR B 244 ARG 0.005 0.000 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 4.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.0730 (tpp) cc_final: -0.0945 (tpp) REVERT: A 315 LYS cc_start: 0.9027 (pttm) cc_final: 0.8806 (pttp) REVERT: A 332 MET cc_start: 0.9309 (mtp) cc_final: 0.8913 (mtp) REVERT: A 449 MET cc_start: 0.9214 (mmm) cc_final: 0.8931 (tpp) REVERT: A 464 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9301 (mm) REVERT: A 466 GLU cc_start: 0.8679 (mp0) cc_final: 0.8379 (mp0) REVERT: A 546 GLU cc_start: 0.8714 (tt0) cc_final: 0.8285 (mt-10) REVERT: B 84 MET cc_start: -0.0323 (tpp) cc_final: -0.0625 (tpp) REVERT: B 217 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9335 (mmtm) REVERT: B 449 MET cc_start: 0.9095 (tpp) cc_final: 0.8814 (tpp) REVERT: B 454 TRP cc_start: 0.9326 (t-100) cc_final: 0.8651 (t-100) REVERT: B 689 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 169 ASP cc_start: 0.1184 (OUTLIER) cc_final: 0.0821 (p0) REVERT: C 315 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8574 (pttp) REVERT: C 464 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9374 (mm) REVERT: C 466 GLU cc_start: 0.8688 (mp0) cc_final: 0.8404 (mp0) REVERT: C 678 MET cc_start: 0.7983 (pmm) cc_final: 0.7728 (pmm) REVERT: D 169 ASP cc_start: 0.0997 (OUTLIER) cc_final: 0.0667 (p0) REVERT: D 203 TYR cc_start: 0.9226 (m-10) cc_final: 0.8947 (m-80) REVERT: D 315 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8701 (pttp) REVERT: D 464 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9301 (mm) REVERT: D 466 GLU cc_start: 0.8769 (mp0) cc_final: 0.8425 (mp0) REVERT: D 550 MET cc_start: 0.7079 (ppp) cc_final: 0.6830 (ppp) REVERT: D 551 TRP cc_start: 0.7336 (t-100) cc_final: 0.6818 (t-100) REVERT: D 689 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8277 (tm-30) REVERT: E 203 TYR cc_start: 0.9151 (m-10) cc_final: 0.8807 (m-80) REVERT: E 315 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8750 (pttp) REVERT: E 464 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9387 (mm) REVERT: E 466 GLU cc_start: 0.8803 (mp0) cc_final: 0.8533 (mp0) REVERT: E 549 THR cc_start: 0.8246 (t) cc_final: 0.7982 (p) REVERT: E 689 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 315 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8654 (pttp) outliers start: 61 outliers final: 47 residues processed: 270 average time/residue: 0.4140 time to fit residues: 194.2314 Evaluate side-chains 263 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 239 optimal weight: 0.3980 chunk 356 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 422 optimal weight: 0.6980 chunk 264 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 327 GLN B 337 GLN E 103 GLN E 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35514 Z= 0.183 Angle : 0.516 9.577 48042 Z= 0.239 Chirality : 0.043 0.146 5436 Planarity : 0.003 0.051 6288 Dihedral : 6.841 59.691 5022 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.86 % Allowed : 13.15 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.36 (0.13), residues: 4398 helix: 1.48 (0.14), residues: 1614 sheet: 1.29 (0.27), residues: 372 loop : -1.82 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 551 HIS 0.002 0.000 HIS F 406 PHE 0.007 0.001 PHE A 742 TYR 0.015 0.001 TYR B 244 ARG 0.003 0.000 ARG F 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 216 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.0700 (tpp) cc_final: -0.0940 (tpp) REVERT: A 327 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8701 (tp-100) REVERT: A 449 MET cc_start: 0.9195 (mmm) cc_final: 0.8894 (tpp) REVERT: A 464 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9324 (mm) REVERT: A 466 GLU cc_start: 0.8747 (mp0) cc_final: 0.8447 (mp0) REVERT: A 546 GLU cc_start: 0.8733 (tt0) cc_final: 0.8307 (mt-10) REVERT: B 84 MET cc_start: -0.0252 (tpp) cc_final: -0.0547 (tpp) REVERT: B 449 MET cc_start: 0.9085 (tpp) cc_final: 0.8825 (tpp) REVERT: B 454 TRP cc_start: 0.9332 (t-100) cc_final: 0.8655 (t-100) REVERT: B 678 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7942 (pmm) REVERT: B 689 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 169 ASP cc_start: 0.1207 (OUTLIER) cc_final: 0.0851 (p0) REVERT: C 315 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8699 (pttp) REVERT: C 464 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9370 (mm) REVERT: C 466 GLU cc_start: 0.8699 (mp0) cc_final: 0.8385 (mp0) REVERT: C 618 PHE cc_start: 0.7880 (t80) cc_final: 0.7298 (t80) REVERT: D 169 ASP cc_start: 0.0806 (OUTLIER) cc_final: 0.0481 (p0) REVERT: D 203 TYR cc_start: 0.9251 (m-10) cc_final: 0.8941 (m-80) REVERT: D 464 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9306 (mm) REVERT: D 466 GLU cc_start: 0.8796 (mp0) cc_final: 0.8434 (mp0) REVERT: D 551 TRP cc_start: 0.7435 (t-100) cc_final: 0.6743 (t-100) REVERT: D 561 GLU cc_start: 0.8032 (pm20) cc_final: 0.7775 (pm20) REVERT: D 689 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 203 TYR cc_start: 0.9119 (m-10) cc_final: 0.8771 (m-80) REVERT: E 315 LYS cc_start: 0.9027 (ptpp) cc_final: 0.8825 (pttt) REVERT: E 464 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9392 (mm) REVERT: E 466 GLU cc_start: 0.8847 (mp0) cc_final: 0.8526 (mp0) REVERT: E 549 THR cc_start: 0.8307 (t) cc_final: 0.8073 (p) REVERT: E 689 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8148 (tm-30) REVERT: F 315 LYS cc_start: 0.9027 (ptpp) cc_final: 0.8647 (pttp) outliers start: 70 outliers final: 53 residues processed: 270 average time/residue: 0.4176 time to fit residues: 196.1505 Evaluate side-chains 277 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 216 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 252 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 268 optimal weight: 0.1980 chunk 287 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 327 GLN B 327 GLN C 296 ASN E 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35514 Z= 0.287 Angle : 0.571 10.663 48042 Z= 0.266 Chirality : 0.044 0.213 5436 Planarity : 0.003 0.058 6288 Dihedral : 7.017 56.752 5022 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.10 % Allowed : 13.26 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.25 (0.13), residues: 4398 helix: 1.49 (0.13), residues: 1662 sheet: 1.34 (0.27), residues: 372 loop : -1.76 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 551 HIS 0.002 0.001 HIS A 406 PHE 0.009 0.001 PHE A 506 TYR 0.026 0.001 TYR B 203 ARG 0.005 0.000 ARG F 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 219 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.0729 (tpp) cc_final: -0.0950 (tpp) REVERT: A 327 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8821 (tp40) REVERT: A 449 MET cc_start: 0.9123 (mmm) cc_final: 0.8856 (tpp) REVERT: A 464 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9390 (mm) REVERT: A 466 GLU cc_start: 0.8846 (mp0) cc_final: 0.8625 (mp0) REVERT: A 546 GLU cc_start: 0.8788 (tt0) cc_final: 0.8549 (mt-10) REVERT: B 84 MET cc_start: -0.0201 (tpp) cc_final: -0.0531 (tpp) REVERT: B 449 MET cc_start: 0.9105 (tpp) cc_final: 0.8740 (tpp) REVERT: B 454 TRP cc_start: 0.9307 (t-100) cc_final: 0.8639 (t-100) REVERT: B 678 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7691 (pmm) REVERT: B 689 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 169 ASP cc_start: 0.1273 (OUTLIER) cc_final: 0.0942 (p0) REVERT: C 315 LYS cc_start: 0.9158 (ptpp) cc_final: 0.8699 (pttp) REVERT: C 449 MET cc_start: 0.9352 (tpp) cc_final: 0.9025 (tpp) REVERT: C 464 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9360 (mm) REVERT: C 466 GLU cc_start: 0.8802 (mp0) cc_final: 0.8401 (mp0) REVERT: C 561 GLU cc_start: 0.8190 (pm20) cc_final: 0.7939 (pm20) REVERT: C 618 PHE cc_start: 0.7983 (t80) cc_final: 0.7334 (t80) REVERT: D 169 ASP cc_start: 0.0888 (OUTLIER) cc_final: 0.0551 (p0) REVERT: D 464 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9311 (mm) REVERT: D 466 GLU cc_start: 0.8885 (mp0) cc_final: 0.8526 (mp0) REVERT: D 551 TRP cc_start: 0.7339 (t-100) cc_final: 0.6942 (t-100) REVERT: D 689 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 203 TYR cc_start: 0.9115 (m-10) cc_final: 0.8652 (m-80) REVERT: E 392 ASP cc_start: 0.9208 (p0) cc_final: 0.9007 (p0) REVERT: E 449 MET cc_start: 0.9177 (mmm) cc_final: 0.8882 (tpp) REVERT: E 464 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9421 (mm) REVERT: E 466 GLU cc_start: 0.8896 (mp0) cc_final: 0.8493 (mp0) REVERT: E 549 THR cc_start: 0.8417 (t) cc_final: 0.8122 (p) REVERT: E 561 GLU cc_start: 0.8138 (pm20) cc_final: 0.7856 (pm20) REVERT: E 689 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 315 LYS cc_start: 0.9056 (ptpp) cc_final: 0.8658 (pttp) REVERT: F 449 MET cc_start: 0.9204 (mmm) cc_final: 0.8682 (tpp) REVERT: F 466 GLU cc_start: 0.8731 (mp0) cc_final: 0.8474 (mp0) outliers start: 79 outliers final: 62 residues processed: 278 average time/residue: 0.4022 time to fit residues: 193.2108 Evaluate side-chains 286 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 216 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 9.9990 chunk 404 optimal weight: 8.9990 chunk 368 optimal weight: 30.0000 chunk 393 optimal weight: 4.9990 chunk 236 optimal weight: 0.4980 chunk 171 optimal weight: 0.6980 chunk 308 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 355 optimal weight: 0.9980 chunk 372 optimal weight: 0.0170 chunk 392 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 327 GLN D 327 GLN E 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35514 Z= 0.152 Angle : 0.520 11.241 48042 Z= 0.241 Chirality : 0.042 0.144 5436 Planarity : 0.003 0.052 6288 Dihedral : 6.777 53.698 5022 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.73 % Allowed : 13.76 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.25 (0.13), residues: 4398 helix: 1.50 (0.13), residues: 1650 sheet: 1.36 (0.27), residues: 372 loop : -1.75 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 551 HIS 0.002 0.000 HIS C 317 PHE 0.010 0.001 PHE A 363 TYR 0.013 0.001 TYR B 244 ARG 0.006 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 221 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9457 (tpp) cc_final: 0.9245 (tpp) REVERT: A 449 MET cc_start: 0.9092 (mmm) cc_final: 0.8831 (tpp) REVERT: A 464 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9391 (mm) REVERT: A 466 GLU cc_start: 0.8779 (mp0) cc_final: 0.8535 (mp0) REVERT: A 546 GLU cc_start: 0.8701 (tt0) cc_final: 0.8244 (mt-10) REVERT: B 84 MET cc_start: -0.0193 (tpp) cc_final: -0.0517 (tpp) REVERT: B 449 MET cc_start: 0.9083 (tpp) cc_final: 0.8747 (tpp) REVERT: B 454 TRP cc_start: 0.9297 (t-100) cc_final: 0.8619 (t-100) REVERT: B 678 MET cc_start: 0.8112 (pmm) cc_final: 0.7820 (pmm) REVERT: B 689 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 740 MET cc_start: 0.9436 (tpp) cc_final: 0.9157 (mmm) REVERT: C 169 ASP cc_start: 0.1265 (OUTLIER) cc_final: 0.0935 (p0) REVERT: C 315 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8712 (pttp) REVERT: C 449 MET cc_start: 0.9356 (tpp) cc_final: 0.8972 (tpp) REVERT: C 464 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9366 (mm) REVERT: C 466 GLU cc_start: 0.8704 (mp0) cc_final: 0.8414 (mp0) REVERT: C 618 PHE cc_start: 0.7867 (t80) cc_final: 0.7259 (t80) REVERT: D 169 ASP cc_start: 0.0882 (OUTLIER) cc_final: 0.0546 (p0) REVERT: D 327 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8743 (tp-100) REVERT: D 464 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9338 (mm) REVERT: D 466 GLU cc_start: 0.8835 (mp0) cc_final: 0.8517 (mp0) REVERT: D 551 TRP cc_start: 0.7369 (t-100) cc_final: 0.6939 (t-100) REVERT: D 689 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 203 TYR cc_start: 0.9103 (m-10) cc_final: 0.8632 (m-80) REVERT: E 315 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8816 (pttp) REVERT: E 392 ASP cc_start: 0.9198 (p0) cc_final: 0.8991 (p0) REVERT: E 466 GLU cc_start: 0.8880 (mp0) cc_final: 0.8503 (mp0) REVERT: E 549 THR cc_start: 0.8420 (t) cc_final: 0.8139 (p) REVERT: E 561 GLU cc_start: 0.8098 (pm20) cc_final: 0.7784 (pm20) REVERT: E 689 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8168 (tm-30) REVERT: F 315 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8764 (pttp) REVERT: F 466 GLU cc_start: 0.8657 (mp0) cc_final: 0.8429 (mp0) outliers start: 65 outliers final: 49 residues processed: 271 average time/residue: 0.4121 time to fit residues: 191.6917 Evaluate side-chains 273 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 218 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 4.9990 chunk 415 optimal weight: 0.0170 chunk 253 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 436 optimal weight: 10.0000 chunk 401 optimal weight: 0.6980 chunk 347 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN D 327 GLN E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35514 Z= 0.194 Angle : 0.533 11.338 48042 Z= 0.246 Chirality : 0.043 0.146 5436 Planarity : 0.003 0.049 6288 Dihedral : 6.753 53.329 5022 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.60 % Allowed : 13.87 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.14 (0.13), residues: 4398 helix: 1.55 (0.13), residues: 1692 sheet: 1.41 (0.27), residues: 372 loop : -1.71 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 551 HIS 0.002 0.000 HIS C 317 PHE 0.013 0.001 PHE A 552 TYR 0.015 0.001 TYR B 244 ARG 0.006 0.000 ARG E 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9483 (tpp) cc_final: 0.9274 (tpp) REVERT: A 449 MET cc_start: 0.9074 (mmm) cc_final: 0.8526 (tpp) REVERT: A 464 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9401 (mm) REVERT: A 466 GLU cc_start: 0.8806 (mp0) cc_final: 0.8556 (mp0) REVERT: A 546 GLU cc_start: 0.8707 (tt0) cc_final: 0.8238 (mt-10) REVERT: B 84 MET cc_start: -0.0174 (tpp) cc_final: -0.0494 (tpp) REVERT: B 449 MET cc_start: 0.9082 (tpp) cc_final: 0.8735 (tpp) REVERT: B 454 TRP cc_start: 0.9312 (t-100) cc_final: 0.8646 (t-100) REVERT: B 678 MET cc_start: 0.8086 (pmm) cc_final: 0.7735 (pmm) REVERT: B 689 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 740 MET cc_start: 0.9456 (tpp) cc_final: 0.9177 (mmm) REVERT: C 169 ASP cc_start: 0.1240 (OUTLIER) cc_final: 0.0906 (p0) REVERT: C 315 LYS cc_start: 0.9176 (ptpp) cc_final: 0.8722 (pttp) REVERT: C 449 MET cc_start: 0.9351 (tpp) cc_final: 0.8986 (tpp) REVERT: C 464 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9433 (mm) REVERT: C 618 PHE cc_start: 0.7836 (t80) cc_final: 0.7227 (t80) REVERT: D 169 ASP cc_start: 0.0899 (OUTLIER) cc_final: 0.0560 (p0) REVERT: D 464 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9398 (mm) REVERT: D 466 GLU cc_start: 0.8833 (mp0) cc_final: 0.8627 (mp0) REVERT: D 551 TRP cc_start: 0.7365 (t-100) cc_final: 0.7014 (t-100) REVERT: D 689 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 203 TYR cc_start: 0.9107 (m-10) cc_final: 0.8641 (m-80) REVERT: E 392 ASP cc_start: 0.9223 (p0) cc_final: 0.9007 (p0) REVERT: E 466 GLU cc_start: 0.8895 (mp0) cc_final: 0.8526 (mp0) REVERT: E 549 THR cc_start: 0.8449 (t) cc_final: 0.8156 (p) REVERT: E 561 GLU cc_start: 0.8186 (pm20) cc_final: 0.7883 (pm20) REVERT: E 689 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 315 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8766 (pttp) REVERT: F 466 GLU cc_start: 0.8691 (mp0) cc_final: 0.8450 (mp0) outliers start: 60 outliers final: 53 residues processed: 268 average time/residue: 0.4274 time to fit residues: 195.1760 Evaluate side-chains 272 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 214 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 8.9990 chunk 370 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN D 337 GLN E 103 GLN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093296 restraints weight = 75863.175| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.78 r_work: 0.2864 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35514 Z= 0.223 Angle : 0.545 11.657 48042 Z= 0.252 Chirality : 0.043 0.147 5436 Planarity : 0.003 0.070 6288 Dihedral : 6.788 57.210 5022 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.70 % Allowed : 13.84 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.11 (0.13), residues: 4398 helix: 1.58 (0.13), residues: 1692 sheet: 1.41 (0.27), residues: 372 loop : -1.70 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 551 HIS 0.002 0.000 HIS C 317 PHE 0.008 0.001 PHE C 552 TYR 0.016 0.001 TYR B 244 ARG 0.006 0.000 ARG E 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6826.85 seconds wall clock time: 124 minutes 50.35 seconds (7490.35 seconds total)