Starting phenix.real_space_refine on Sat Jul 27 00:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/07_2024/7rlc_24525_neut.cif" } resolution = 3.2 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= 0.069 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 21894 2.51 5 N 6144 2.21 5 O 6702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.59s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 34980 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 5766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5766 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: 19.47, per 1000 atoms: 0.56 Number of scatterers: 34980 At special positions: 0 Unit cell: (179.837, 169.784, 120.636, 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 6702 8.00 N 6144 7.00 C 21894 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: 12.49 Conformation dependent library (CDL) restraints added in 6.4 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... Secondary structure from input PDB file: 198 helices and 12 sheets defined 41.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.067A pdb=" N GLU A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 190 through 197 removed outlier: 4.397A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.670A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.527A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.527A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.998A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.649A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.503A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.685A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.602A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 4.211A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.583A pdb=" N ASP A 478 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.568A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.540A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.842A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.659A pdb=" N PHE A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 587 removed outlier: 3.972A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.517A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.686A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.686A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 removed outlier: 4.067A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 679' Processing helix chain 'A' and resid 683 through 695 Processing helix chain 'A' and resid 695 through 705 removed outlier: 3.944A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.629A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 739 " --> pdb=" O HIS A 735 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.618A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.939A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.067A pdb=" N GLU B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 190 through 197 removed outlier: 4.397A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.670A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.526A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.528A pdb=" N ILE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.998A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.649A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.503A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.684A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.603A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 removed outlier: 4.211A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.583A pdb=" N ASP B 478 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.567A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 503 Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.540A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.843A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.658A pdb=" N PHE B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 587 removed outlier: 3.972A pdb=" N ALA B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.517A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.685A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.686A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 removed outlier: 4.067A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 679' Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 695 through 705 removed outlier: 3.945A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 removed outlier: 3.629A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 739 " --> pdb=" O HIS B 735 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.617A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.939A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.066A pdb=" N GLU C 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 190 through 197 removed outlier: 4.398A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.670A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.526A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.527A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.998A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.649A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.504A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.684A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.602A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 4.212A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.583A pdb=" N ASP C 478 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 491 removed outlier: 3.568A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 500 through 503 Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.540A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.843A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.658A pdb=" N PHE C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 587 removed outlier: 3.972A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.517A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.686A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.685A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 656 " --> pdb=" O SER C 652 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 679 removed outlier: 4.067A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 679' Processing helix chain 'C' and resid 683 through 695 Processing helix chain 'C' and resid 695 through 705 removed outlier: 3.944A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.630A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET C 740 " --> pdb=" O PHE C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.617A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 757 " --> pdb=" O ARG C 753 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.938A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.067A pdb=" N GLU D 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 190 through 197 removed outlier: 4.397A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.670A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.527A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.527A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.998A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.649A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.503A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.685A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.603A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 removed outlier: 4.211A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 453 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.583A pdb=" N ASP D 478 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.568A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 500 through 503 Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.540A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.844A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.659A pdb=" N PHE D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 587 removed outlier: 3.973A pdb=" N ALA D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.516A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.686A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.685A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 656 " --> pdb=" O SER D 652 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 657 " --> pdb=" O ARG D 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 658 " --> pdb=" O VAL D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 679 removed outlier: 4.067A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 673 through 679' Processing helix chain 'D' and resid 683 through 695 Processing helix chain 'D' and resid 695 through 705 removed outlier: 3.944A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 740 removed outlier: 3.630A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA D 739 " --> pdb=" O HIS D 735 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET D 740 " --> pdb=" O PHE D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.617A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 757 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.938A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 4.067A pdb=" N GLU E 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 190 through 197 removed outlier: 4.397A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.671A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 221 removed outlier: 3.527A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.527A pdb=" N ILE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.998A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.648A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 removed outlier: 3.503A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.684A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.603A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 4.211A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 453 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.584A pdb=" N ASP E 478 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 491 removed outlier: 3.568A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 500 through 503 Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.539A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.843A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.658A pdb=" N PHE E 563 " --> pdb=" O VAL E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 587 removed outlier: 3.972A pdb=" N ALA E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.516A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.686A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.685A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 658 " --> pdb=" O VAL E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 679 removed outlier: 4.067A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 673 through 679' Processing helix chain 'E' and resid 683 through 695 Processing helix chain 'E' and resid 695 through 705 removed outlier: 3.944A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 740 removed outlier: 3.628A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET E 740 " --> pdb=" O PHE E 736 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.617A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 757 " --> pdb=" O ARG E 753 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.938A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.067A pdb=" N GLU F 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 190 through 197 removed outlier: 4.398A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.671A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 221 removed outlier: 3.527A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.853A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.528A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.997A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 318 through 333 removed outlier: 3.650A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.503A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.685A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.603A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 removed outlier: 4.210A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 453 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.583A pdb=" N ASP F 478 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 491 removed outlier: 3.568A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 500 through 503 Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.540A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.843A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.658A pdb=" N PHE F 563 " --> pdb=" O VAL F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 587 removed outlier: 3.972A pdb=" N ALA F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.517A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.686A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.686A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 657 " --> pdb=" O ARG F 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 658 " --> pdb=" O VAL F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 679 removed outlier: 4.066A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 673 through 679' Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 695 through 705 removed outlier: 3.945A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 740 removed outlier: 3.629A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET F 740 " --> pdb=" O PHE F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.618A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 757 " --> pdb=" O ARG F 753 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.939A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.276A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.466A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 622 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.275A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.467A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 622 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.276A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.465A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 622 " --> pdb=" O PHE C 576 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.276A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.465A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 622 " --> pdb=" O PHE D 576 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.276A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.466A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 622 " --> pdb=" O PHE E 576 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.276A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.466A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 622 " --> pdb=" O PHE F 576 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2178 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: 11.06 Time building geometry restraints manager: 13.81 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: 12097 1.37 - 1.52: 9084 1.52 - 1.66: 14069 1.66 - 1.80: 166 1.80 - 1.95: 134 Bond restraints: 35550 Sorted by residual: bond pdb=" CB GLU B 466 " pdb=" CG GLU B 466 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU C 466 " pdb=" CG GLU C 466 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU E 466 " pdb=" CG GLU E 466 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU A 466 " pdb=" CG GLU A 466 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB GLU D 466 " pdb=" CG GLU D 466 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 35545 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.07: 762 105.07 - 112.30: 17391 112.30 - 119.53: 13357 119.53 - 126.76: 16168 126.76 - 133.98: 406 Bond angle restraints: 48084 Sorted by residual: angle pdb=" N VAL E 94 " pdb=" CA VAL E 94 " pdb=" C VAL E 94 " ideal model delta sigma weight residual 113.71 109.49 4.22 9.50e-01 1.11e+00 1.97e+01 angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 113.71 109.49 4.22 9.50e-01 1.11e+00 1.97e+01 angle pdb=" N VAL C 94 " pdb=" CA VAL C 94 " pdb=" C VAL C 94 " ideal model delta sigma weight residual 113.71 109.50 4.21 9.50e-01 1.11e+00 1.96e+01 angle pdb=" N VAL F 94 " pdb=" CA VAL F 94 " pdb=" C VAL F 94 " ideal model delta sigma weight residual 113.71 109.51 4.20 9.50e-01 1.11e+00 1.95e+01 angle pdb=" N VAL D 94 " pdb=" CA VAL D 94 " pdb=" C VAL D 94 " ideal model delta sigma weight residual 113.71 109.53 4.18 9.50e-01 1.11e+00 1.94e+01 ... (remaining 48079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.78: 20335 12.78 - 25.56: 1139 25.56 - 38.34: 444 38.34 - 51.12: 132 51.12 - 63.90: 36 Dihedral angle restraints: 22086 sinusoidal: 9366 harmonic: 12720 Sorted by residual: dihedral pdb=" CA MET F 508 " pdb=" C MET F 508 " pdb=" N THR F 509 " pdb=" CA THR F 509 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA MET E 508 " pdb=" C MET E 508 " pdb=" N THR E 509 " pdb=" CA THR E 509 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA MET C 508 " pdb=" C MET C 508 " pdb=" N THR C 509 " pdb=" CA THR C 509 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 22083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2748 0.026 - 0.052: 1673 0.052 - 0.078: 536 0.078 - 0.104: 307 0.104 - 0.131: 172 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CA ILE D 353 " pdb=" N ILE D 353 " pdb=" C ILE D 353 " pdb=" CB ILE D 353 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE F 353 " pdb=" N ILE F 353 " pdb=" C ILE F 353 " pdb=" CB ILE F 353 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE E 353 " pdb=" N ILE E 353 " pdb=" C ILE E 353 " pdb=" CB ILE E 353 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 5433 not shown) Planarity restraints: 6294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 551 " -0.024 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP C 551 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP C 551 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 551 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 551 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 551 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 551 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 551 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 551 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 551 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 551 " -0.024 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP D 551 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP D 551 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 551 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 551 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 551 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 551 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 551 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 551 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 551 " 0.024 2.00e-02 2.50e+03 2.27e-02 1.28e+01 pdb=" CG TRP F 551 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 551 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 551 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 551 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 551 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 551 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 551 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 551 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 551 " 0.000 2.00e-02 2.50e+03 ... (remaining 6291 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 10 1.69 - 2.49: 135 2.49 - 3.30: 36890 3.30 - 4.10: 76054 4.10 - 4.90: 133958 Warning: very small nonbonded interaction distances. Nonbonded interactions: 247047 Sorted by model distance: nonbonded pdb=" O1B AGS E 901 " pdb="MG MG E 903 " model vdw 0.891 2.170 nonbonded pdb=" O1B AGS C 901 " pdb="MG MG C 903 " model vdw 0.976 2.170 nonbonded pdb=" O1B AGS B 901 " pdb="MG MG B 903 " model vdw 1.045 2.170 nonbonded pdb=" O1B AGS D 901 " pdb="MG MG D 903 " model vdw 1.133 2.170 nonbonded pdb=" CD1 ILE C 269 " pdb=" CG1 ILE C 303 " model vdw 1.515 3.860 ... (remaining 247042 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 1.490 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 87.230 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.170 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 0.041 35550 Z= 0.165 Angle : 0.652 11.504 48084 Z= 0.358 Chirality : 0.042 0.131 5436 Planarity : 0.004 0.054 6294 Dihedral : 10.105 63.903 13842 Min Nonbonded Distance : 0.891 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % 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: -1.71 (0.12), residues: 4398 helix: -0.61 (0.15), residues: 1242 sheet: 1.27 (0.27), residues: 408 loop : -1.87 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP C 551 HIS 0.021 0.002 HIS D 499 PHE 0.011 0.001 PHE D 265 TYR 0.005 0.001 TYR E 755 ARG 0.008 0.000 ARG F 599 *********************** 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 192 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 4.518 Fit side-chains REVERT: B 305 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8653 (mt-10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3863 time to fit residues: 132.8106 Evaluate side-chains 163 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 50.0000 chunk 331 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 223 optimal weight: 50.0000 chunk 177 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 397 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 327 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS A 602 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 602 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 35550 Z= 0.453 Angle : 0.705 8.296 48084 Z= 0.356 Chirality : 0.050 0.195 5436 Planarity : 0.005 0.057 6294 Dihedral : 7.753 66.067 5028 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.62 % Favored : 93.11 % Rotamer: Outliers : 2.39 % Allowed : 9.09 % Favored : 88.52 % 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: -1.79 (0.12), residues: 4398 helix: -0.69 (0.13), residues: 1542 sheet: 0.91 (0.25), residues: 408 loop : -1.95 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP D 551 HIS 0.006 0.001 HIS A 404 PHE 0.022 0.002 PHE C 768 TYR 0.017 0.002 TYR D 644 ARG 0.012 0.001 ARG E 377 *********************** 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 226 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 136 time to evaluate : 4.019 Fit side-chains REVERT: B 158 MET cc_start: 0.3242 (pmm) cc_final: 0.2882 (pmm) REVERT: B 599 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6900 (mpp-170) REVERT: D 153 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5727 (tm) REVERT: D 158 MET cc_start: 0.2985 (pmm) cc_final: 0.2619 (pmm) REVERT: E 153 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5249 (tm) REVERT: E 442 MET cc_start: 0.8842 (mmm) cc_final: 0.8529 (mmp) REVERT: F 153 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5762 (tm) REVERT: F 599 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6843 (mpp-170) outliers start: 90 outliers final: 38 residues processed: 209 average time/residue: 0.4018 time to fit residues: 143.8975 Evaluate side-chains 174 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 10.0000 chunk 123 optimal weight: 0.0470 chunk 331 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 398 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 354 optimal weight: 0.0870 chunk 395 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 319 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 285 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35550 Z= 0.129 Angle : 0.472 7.909 48084 Z= 0.227 Chirality : 0.042 0.129 5436 Planarity : 0.003 0.056 6294 Dihedral : 6.900 60.614 5028 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 9.91 % Favored : 88.68 % 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: -1.23 (0.12), residues: 4398 helix: -0.04 (0.14), residues: 1560 sheet: 1.43 (0.25), residues: 384 loop : -1.78 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 551 HIS 0.002 0.000 HIS D 384 PHE 0.009 0.001 PHE F 503 TYR 0.008 0.001 TYR F 244 ARG 0.010 0.000 ARG A 599 *********************** 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 182 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 4.048 Fit side-chains REVERT: B 158 MET cc_start: 0.3247 (pmm) cc_final: 0.2874 (pmm) REVERT: B 599 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: D 158 MET cc_start: 0.2606 (pmm) cc_final: 0.2200 (pmm) REVERT: F 442 MET cc_start: 0.8625 (mmp) cc_final: 0.8337 (mmp) REVERT: F 599 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5376 (mpp-170) outliers start: 53 outliers final: 29 residues processed: 175 average time/residue: 0.4135 time to fit residues: 127.3979 Evaluate side-chains 159 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.0870 chunk 299 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 379 optimal weight: 0.5980 chunk 114 optimal weight: 0.0970 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35550 Z= 0.147 Angle : 0.463 7.470 48084 Z= 0.221 Chirality : 0.042 0.126 5436 Planarity : 0.003 0.054 6294 Dihedral : 6.487 59.045 5028 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 1.44 % Allowed : 10.13 % Favored : 88.44 % 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: -0.84 (0.13), residues: 4398 helix: 0.47 (0.14), residues: 1530 sheet: 1.50 (0.25), residues: 402 loop : -1.67 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 551 HIS 0.002 0.000 HIS B 404 PHE 0.012 0.001 PHE B 552 TYR 0.007 0.001 TYR F 244 ARG 0.005 0.000 ARG C 599 *********************** 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 185 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 131 time to evaluate : 3.943 Fit side-chains REVERT: A 640 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: B 158 MET cc_start: 0.3531 (pmm) cc_final: 0.3093 (pmm) REVERT: C 599 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5005 (mpp-170) REVERT: D 153 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5535 (tm) REVERT: D 158 MET cc_start: 0.2658 (pmm) cc_final: 0.2231 (pmm) REVERT: E 153 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5349 (tm) REVERT: E 442 MET cc_start: 0.8912 (mmp) cc_final: 0.8630 (mmp) REVERT: F 153 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5462 (tm) REVERT: F 599 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5379 (mpp-170) outliers start: 54 outliers final: 38 residues processed: 174 average time/residue: 0.4181 time to fit residues: 126.6818 Evaluate side-chains 171 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 8.9990 chunk 240 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 380 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35550 Z= 0.232 Angle : 0.504 7.377 48084 Z= 0.245 Chirality : 0.044 0.133 5436 Planarity : 0.004 0.054 6294 Dihedral : 6.523 59.203 5028 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 1.49 % Allowed : 9.94 % Favored : 88.57 % 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: -0.67 (0.13), residues: 4398 helix: 0.60 (0.14), residues: 1566 sheet: 1.36 (0.25), residues: 408 loop : -1.55 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 551 HIS 0.003 0.001 HIS C 404 PHE 0.012 0.001 PHE C 363 TYR 0.008 0.001 TYR F 517 ARG 0.004 0.000 ARG C 599 *********************** 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 185 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 3.932 Fit side-chains REVERT: B 158 MET cc_start: 0.3499 (pmm) cc_final: 0.3046 (pmm) REVERT: B 599 ARG cc_start: 0.6786 (ptp90) cc_final: 0.6513 (ptp90) REVERT: C 599 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5098 (mpp-170) REVERT: D 153 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5521 (tm) REVERT: D 158 MET cc_start: 0.2811 (pmm) cc_final: 0.2373 (pmm) REVERT: E 46 MET cc_start: 0.5912 (mmm) cc_final: 0.5105 (mmm) REVERT: E 153 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5359 (tm) REVERT: F 153 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5375 (tm) REVERT: F 599 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5515 (mpp-170) outliers start: 56 outliers final: 32 residues processed: 175 average time/residue: 0.4101 time to fit residues: 125.7784 Evaluate side-chains 164 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.3057 > 50: distance: 84 - 89: 21.512 distance: 89 - 90: 24.976 distance: 90 - 91: 20.970 distance: 90 - 93: 20.309 distance: 91 - 92: 4.076 distance: 91 - 95: 43.812 distance: 93 - 94: 19.460 distance: 95 - 101: 3.609 distance: 96 - 97: 36.522 distance: 96 - 99: 4.189 distance: 97 - 98: 26.459 distance: 97 - 102: 13.185 distance: 99 - 100: 5.438 distance: 100 - 101: 3.323 distance: 102 - 103: 25.947 distance: 103 - 104: 16.376 distance: 103 - 106: 21.201 distance: 104 - 105: 22.009 distance: 104 - 114: 24.533 distance: 106 - 107: 4.358 distance: 107 - 108: 32.256 distance: 107 - 109: 8.329 distance: 108 - 110: 14.349 distance: 109 - 111: 12.318 distance: 110 - 112: 5.901 distance: 111 - 112: 25.659 distance: 112 - 113: 16.884 distance: 114 - 115: 18.992 distance: 115 - 118: 27.208 distance: 116 - 117: 43.314 distance: 116 - 120: 10.512 distance: 118 - 119: 32.757 distance: 120 - 121: 23.004 distance: 121 - 122: 34.773 distance: 121 - 124: 21.088 distance: 122 - 123: 28.789 distance: 122 - 128: 33.643 distance: 124 - 125: 13.836 distance: 124 - 126: 30.838 distance: 125 - 127: 25.639 distance: 128 - 129: 48.995 distance: 129 - 130: 58.059 distance: 129 - 132: 35.811 distance: 130 - 131: 49.909 distance: 130 - 135: 23.772 distance: 132 - 133: 13.827 distance: 132 - 134: 6.202 distance: 135 - 136: 23.431 distance: 136 - 137: 34.767 distance: 136 - 139: 13.276 distance: 137 - 138: 40.694 distance: 137 - 140: 38.209 distance: 140 - 141: 35.160 distance: 140 - 146: 55.216 distance: 141 - 142: 37.052 distance: 141 - 144: 55.417 distance: 142 - 143: 11.866 distance: 142 - 147: 32.591 distance: 144 - 145: 7.430 distance: 145 - 146: 34.458 distance: 147 - 148: 17.318 distance: 148 - 149: 36.640 distance: 148 - 151: 7.378 distance: 149 - 150: 43.877 distance: 149 - 155: 10.803 distance: 151 - 152: 19.857 distance: 152 - 153: 16.108 distance: 152 - 154: 18.165 distance: 155 - 156: 9.045 distance: 156 - 157: 10.078 distance: 156 - 159: 13.329 distance: 157 - 158: 15.310 distance: 157 - 162: 25.284 distance: 159 - 160: 21.133 distance: 159 - 161: 31.558