Starting phenix.real_space_refine on Thu Feb 22 18:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/02_2024/7rlc_24525_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/02_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_24525/02_2024/7rlc_24525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/02_2024/7rlc_24525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/02_2024/7rlc_24525_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlc_24525/02_2024/7rlc_24525_updated.pdb" } 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18.45, per 1000 atoms: 0.53 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: 11.96 Conformation dependent library (CDL) restraints added in 6.1 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 12 sheets defined 34.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.811A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.512A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.649A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.503A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.728A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.700A 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) removed outlier: 3.918A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.568A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 524 through 535 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 544 through 550 removed outlier: 3.697A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.370A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.734A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 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 674 through 678 removed outlier: 3.701A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 674 through 678' Processing helix chain 'A' and resid 684 through 704 removed outlier: 4.014A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 742 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) removed outlier: 4.527A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.813A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.513A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.649A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.503A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.728A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.700A 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) removed outlier: 3.918A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.567A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 524 through 535 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 544 through 550 removed outlier: 3.697A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 580 through 586 removed outlier: 4.371A pdb=" N ARG B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.733A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 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 674 through 678 removed outlier: 3.700A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 678' Processing helix chain 'B' and resid 684 through 704 removed outlier: 4.015A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 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) removed outlier: 4.526A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 44 through 47 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 191 through 198 removed outlier: 3.811A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.512A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.649A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.504A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.728A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.700A 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) removed outlier: 3.918A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.568A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 524 through 535 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 544 through 550 removed outlier: 3.696A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 580 through 586 removed outlier: 4.370A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.733A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 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 674 through 678 removed outlier: 3.701A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 674 through 678' Processing helix chain 'C' and resid 684 through 704 removed outlier: 4.015A pdb=" N LYS C 696 " --> pdb=" O GLN C 692 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 742 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) removed outlier: 4.526A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 44 through 47 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.811A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.513A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.649A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.503A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.728A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.701A 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) removed outlier: 3.918A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 491 removed outlier: 3.568A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 524 through 535 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 544 through 550 removed outlier: 3.697A pdb=" N LEU D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 580 through 586 removed outlier: 4.370A pdb=" N ARG D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 removed outlier: 3.734A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 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 674 through 678 removed outlier: 3.700A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 674 through 678' Processing helix chain 'D' and resid 684 through 704 removed outlier: 4.015A pdb=" N LYS D 696 " --> pdb=" O GLN D 692 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 742 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) removed outlier: 4.527A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 44 through 47 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 191 through 198 removed outlier: 3.811A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.513A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 275 No H-bonds generated for 'chain 'E' and resid 272 through 275' Processing helix chain 'E' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 319 through 332 removed outlier: 3.648A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 384 removed outlier: 3.503A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.729A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.700A 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) removed outlier: 3.918A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 491 removed outlier: 3.568A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'E' and resid 524 through 535 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 544 through 550 removed outlier: 3.697A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 568 Processing helix chain 'E' and resid 580 through 586 removed outlier: 4.369A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 removed outlier: 3.733A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 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 674 through 678 removed outlier: 3.702A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 674 through 678' Processing helix chain 'E' and resid 684 through 704 removed outlier: 4.014A pdb=" N LYS E 696 " --> pdb=" O GLN E 692 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 697 " --> pdb=" O ARG E 693 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA E 698 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 742 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) removed outlier: 4.527A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 44 through 47 Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 191 through 198 removed outlier: 3.811A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 220 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 233 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 251 through 258 removed outlier: 3.513A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 275 No H-bonds generated for 'chain 'F' and resid 272 through 275' Processing helix chain 'F' and resid 281 through 293 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 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 319 through 332 removed outlier: 3.650A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 384 removed outlier: 3.503A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 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 408 through 426 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) removed outlier: 4.727A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.700A 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) removed outlier: 3.918A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 491 removed outlier: 3.568A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 524 through 535 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 544 through 550 removed outlier: 3.697A pdb=" N LEU F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 580 through 586 removed outlier: 4.369A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 removed outlier: 3.734A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 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 674 through 678 removed outlier: 3.701A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 674 through 678' Processing helix chain 'F' and resid 684 through 704 removed outlier: 4.014A pdb=" N LYS F 696 " --> pdb=" O GLN F 692 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 697 " --> pdb=" O ARG F 693 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA F 698 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 742 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) removed outlier: 4.526A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 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 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 365 through 369 removed outlier: 3.532A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (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: 6.276A 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) Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.526A pdb=" N ILE A 645 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 622 " --> pdb=" O PHE A 576 " (cutoff:3.500A) 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) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 369 removed outlier: 3.532A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (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: 6.275A 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) Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.525A pdb=" N ILE B 645 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 622 " --> pdb=" O PHE B 576 " (cutoff:3.500A) 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) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 369 removed outlier: 3.533A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLY C 245 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 347 " --> pdb=" O GLY C 245 " (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: 6.276A 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) Processing sheet with id= F, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.525A pdb=" N ILE C 645 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 622 " --> pdb=" O PHE C 576 " (cutoff:3.500A) 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) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 369 removed outlier: 3.533A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (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: 6.276A 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) Processing sheet with id= H, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.525A pdb=" N ILE D 645 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 622 " --> pdb=" O PHE D 576 " (cutoff:3.500A) 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) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 369 removed outlier: 3.532A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (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: 6.276A 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) Processing sheet with id= J, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.526A pdb=" N ILE E 645 " --> pdb=" O TYR E 517 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 622 " --> pdb=" O PHE E 576 " (cutoff:3.500A) 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) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 369 removed outlier: 3.532A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY F 245 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR F 347 " --> pdb=" O GLY F 245 " (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: 6.276A 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) Processing sheet with id= L, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.525A pdb=" N ILE F 645 " --> pdb=" O TYR F 517 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 622 " --> pdb=" O PHE F 576 " (cutoff:3.500A) 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) 648 hydrogen bonds defined for protein. 1872 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: 9.81 Time building geometry restraints manager: 13.15 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: 36974 3.30 - 4.10: 76312 4.10 - 4.90: 134216 Warning: very small nonbonded interaction distances. Nonbonded interactions: 247647 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 247642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.020 Extract box with map and model: 5.450 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 82.170 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.220 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.560 ------------------------------------------------------------------------------- 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= 0.169 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 : 4.235 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: 0.3895 time to fit residues: 134.0330 Evaluate side-chains 163 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.793 ------------------------------------------------------------------------------- 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: 9.9990 chunk 184 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 223 optimal weight: 50.0000 chunk 177 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 384 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 35550 Z= 0.463 Angle : 0.727 11.057 48084 Z= 0.372 Chirality : 0.052 0.579 5436 Planarity : 0.005 0.058 6294 Dihedral : 7.884 66.528 5028 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.43 % Favored : 93.29 % Rotamer: Outliers : 2.34 % Allowed : 9.17 % Favored : 88.49 % 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: -1.75 (0.12), residues: 4398 helix: -0.76 (0.13), residues: 1434 sheet: 0.95 (0.25), residues: 414 loop : -1.83 (0.11), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP D 551 HIS 0.006 0.001 HIS A 404 PHE 0.025 0.003 PHE B 575 TYR 0.022 0.002 TYR A 517 ARG 0.015 0.001 ARG E 358 *********************** 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 224 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 136 time to evaluate : 4.323 Fit side-chains REVERT: A 599 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6816 (mpp-170) REVERT: B 158 MET cc_start: 0.3295 (pmm) cc_final: 0.2926 (pmm) REVERT: B 599 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6864 (mpp-170) REVERT: C 599 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6746 (mpp-170) REVERT: D 153 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5702 (tm) REVERT: D 158 MET cc_start: 0.2993 (pmm) cc_final: 0.2600 (pmm) REVERT: D 608 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: E 153 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5307 (tm) REVERT: E 640 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: F 153 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5600 (tm) REVERT: F 599 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6929 (mpp-170) outliers start: 88 outliers final: 39 residues processed: 207 average time/residue: 0.4272 time to fit residues: 152.6637 Evaluate side-chains 178 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 3.912 ------------------------------------------------------------------------------- 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 A residue 599 ARG 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 599 ARG 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 278 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 D residue 608 MET Chi-restraints excluded: chain E residue 16 ILE 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 E residue 640 ASP Chi-restraints excluded: chain F residue 16 ILE 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: 7.9990 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 0.4980 chunk 270 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 395 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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** A 602 ASN 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** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7963 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35550 Z= 0.212 Angle : 0.495 7.391 48084 Z= 0.242 Chirality : 0.043 0.124 5436 Planarity : 0.004 0.056 6294 Dihedral : 7.353 60.791 5028 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 9.84 % 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: -1.22 (0.12), residues: 4398 helix: 0.02 (0.14), residues: 1452 sheet: 1.29 (0.25), residues: 414 loop : -1.76 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 551 HIS 0.003 0.001 HIS D 384 PHE 0.014 0.001 PHE E 503 TYR 0.007 0.001 TYR F 244 ARG 0.010 0.000 ARG E 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 184 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 4.287 Fit side-chains REVERT: A 599 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.5338 (mpp-170) REVERT: B 158 MET cc_start: 0.3346 (pmm) cc_final: 0.2937 (pmm) REVERT: B 599 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6689 (ptp90) REVERT: C 599 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.5175 (mpp-170) REVERT: D 158 MET cc_start: 0.2735 (pmm) cc_final: 0.2307 (pmm) REVERT: E 442 MET cc_start: 0.9004 (mmp) cc_final: 0.8712 (mmp) REVERT: F 46 MET cc_start: 0.6145 (mmm) cc_final: 0.5818 (mmm) REVERT: F 442 MET cc_start: 0.8708 (mmp) cc_final: 0.8485 (mmp) REVERT: F 599 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.5490 (mpp-170) outliers start: 56 outliers final: 29 residues processed: 178 average time/residue: 0.4139 time to fit residues: 128.7412 Evaluate side-chains 161 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE 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 599 ARG 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 599 ARG Chi-restraints excluded: chain C residue 16 ILE 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 C residue 599 ARG Chi-restraints excluded: chain D residue 133 VAL 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 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 468 VAL 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: 3.9990 chunk 299 optimal weight: 30.0000 chunk 206 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 399 optimal weight: 8.9990 chunk 423 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35550 Z= 0.315 Angle : 0.564 7.031 48084 Z= 0.274 Chirality : 0.046 0.226 5436 Planarity : 0.004 0.058 6294 Dihedral : 7.471 61.220 5028 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 1.70 % Allowed : 9.76 % Favored : 88.54 % 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: -1.02 (0.12), residues: 4398 helix: 0.23 (0.14), residues: 1464 sheet: 1.32 (0.24), residues: 414 loop : -1.66 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 551 HIS 0.004 0.001 HIS B 404 PHE 0.018 0.002 PHE C 552 TYR 0.008 0.001 TYR A 644 ARG 0.005 0.000 ARG D 377 *********************** 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 197 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 133 time to evaluate : 4.311 Fit side-chains REVERT: A 551 TRP cc_start: 0.6429 (t60) cc_final: 0.6171 (t60) REVERT: A 599 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5429 (mpp-170) REVERT: B 158 MET cc_start: 0.3195 (pmm) cc_final: 0.2766 (pmm) REVERT: C 599 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5262 (mpp-170) REVERT: D 153 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5526 (tm) REVERT: D 158 MET cc_start: 0.2882 (pmm) cc_final: 0.2435 (pmm) REVERT: E 153 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5347 (tm) REVERT: F 46 MET cc_start: 0.6003 (mmm) cc_final: 0.5709 (mmm) REVERT: F 153 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5361 (tm) REVERT: F 599 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.5472 (mpp-170) outliers start: 64 outliers final: 35 residues processed: 187 average time/residue: 0.4258 time to fit residues: 138.6106 Evaluate side-chains 171 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 4.158 ------------------------------------------------------------------------------- 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 364 ASP 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 599 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 364 ASP 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 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 640 ASP 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 352 SER Chi-restraints excluded: chain D residue 364 ASP 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 16 ILE 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 599 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 chunk 380 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** 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: 0.7992 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35550 Z= 0.261 Angle : 0.510 8.858 48084 Z= 0.247 Chirality : 0.044 0.157 5436 Planarity : 0.004 0.059 6294 Dihedral : 7.103 59.972 5028 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 9.86 % Favored : 88.54 % 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: -0.79 (0.13), residues: 4398 helix: 0.46 (0.14), residues: 1482 sheet: 1.42 (0.24), residues: 414 loop : -1.54 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 551 HIS 0.004 0.001 HIS E 406 PHE 0.012 0.001 PHE D 503 TYR 0.007 0.001 TYR F 244 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 194 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 134 time to evaluate : 3.993 Fit side-chains REVERT: A 551 TRP cc_start: 0.6363 (t60) cc_final: 0.6139 (t60) REVERT: A 599 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5587 (mpp-170) REVERT: B 158 MET cc_start: 0.2981 (pmm) cc_final: 0.2551 (pmm) REVERT: C 599 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.5188 (mpp-170) REVERT: D 153 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5506 (tm) REVERT: D 158 MET cc_start: 0.2596 (pmm) cc_final: 0.2129 (pmm) REVERT: E 46 MET cc_start: 0.5835 (mmm) cc_final: 0.5283 (mmm) REVERT: E 153 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5343 (tm) REVERT: E 599 ARG cc_start: 0.6788 (ptp90) cc_final: 0.6525 (ptp90) REVERT: F 46 MET cc_start: 0.6004 (mmm) cc_final: 0.5716 (mmm) REVERT: F 153 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5301 (tm) REVERT: F 344 MET cc_start: 0.8832 (mtp) cc_final: 0.8532 (mtm) REVERT: F 599 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5296 (mpp-170) outliers start: 60 outliers final: 36 residues processed: 184 average time/residue: 0.4620 time to fit residues: 145.9728 Evaluate side-chains 172 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 4.088 ------------------------------------------------------------------------------- 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 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 464 LEU 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 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG 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 364 ASP 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 364 ASP 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 16 ILE 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 599 ARG Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 9.9990 chunk 381 optimal weight: 30.0000 chunk 83 optimal weight: 0.3980 chunk 248 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 423 optimal weight: 10.0000 chunk 351 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 222 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35550 Z= 0.134 Angle : 0.458 9.619 48084 Z= 0.218 Chirality : 0.042 0.132 5436 Planarity : 0.003 0.060 6294 Dihedral : 6.710 59.000 5028 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.07 % Favored : 95.79 % Rotamer: Outliers : 1.38 % Allowed : 10.26 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4398 helix: 0.78 (0.14), residues: 1470 sheet: 1.78 (0.25), residues: 390 loop : -1.44 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 551 HIS 0.002 0.000 HIS E 340 PHE 0.007 0.001 PHE D 503 TYR 0.008 0.001 TYR F 244 ARG 0.003 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 134 time to evaluate : 3.728 Fit side-chains REVERT: A 599 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.5380 (mpp-170) REVERT: B 158 MET cc_start: 0.2518 (pmm) cc_final: 0.2083 (pmm) REVERT: C 599 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.4980 (mpp-170) REVERT: D 153 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5498 (tm) REVERT: D 158 MET cc_start: 0.2657 (pmm) cc_final: 0.2200 (pmm) REVERT: E 46 MET cc_start: 0.5995 (mmm) cc_final: 0.5580 (mmm) REVERT: E 153 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5340 (tm) REVERT: E 599 ARG cc_start: 0.6746 (ptp90) cc_final: 0.6476 (ptp90) REVERT: F 153 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5309 (tm) REVERT: F 599 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5354 (mpp-170) outliers start: 52 outliers final: 27 residues processed: 175 average time/residue: 0.4204 time to fit residues: 126.1169 Evaluate side-chains 163 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 3.705 ------------------------------------------------------------------------------- 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 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG 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 464 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 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 16 ILE 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 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 309 optimal weight: 30.0000 chunk 239 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 422 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35550 Z= 0.426 Angle : 0.629 10.782 48084 Z= 0.305 Chirality : 0.048 0.146 5436 Planarity : 0.004 0.060 6294 Dihedral : 7.044 59.427 5028 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 1.78 % Allowed : 9.99 % Favored : 88.22 % 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: -0.66 (0.13), residues: 4398 helix: 0.52 (0.14), residues: 1476 sheet: 1.42 (0.25), residues: 414 loop : -1.41 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 551 HIS 0.005 0.001 HIS F 406 PHE 0.015 0.002 PHE B 363 TYR 0.006 0.001 TYR C 495 ARG 0.008 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 130 time to evaluate : 3.806 Fit side-chains REVERT: A 551 TRP cc_start: 0.6373 (t60) cc_final: 0.6103 (t60) REVERT: A 599 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.5593 (mpp-170) REVERT: B 158 MET cc_start: 0.2795 (pmm) cc_final: 0.2347 (pmm) REVERT: C 599 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6552 (mpp-170) REVERT: D 153 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5490 (tm) REVERT: D 158 MET cc_start: 0.2683 (pmm) cc_final: 0.2220 (pmm) REVERT: E 153 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5378 (tm) REVERT: F 153 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5270 (tm) outliers start: 67 outliers final: 35 residues processed: 188 average time/residue: 0.4347 time to fit residues: 140.4704 Evaluate side-chains 168 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 3.871 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 695 CYS 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 364 ASP 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 D residue 601 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 364 ASP Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35550 Z= 0.243 Angle : 0.510 10.302 48084 Z= 0.246 Chirality : 0.044 0.138 5436 Planarity : 0.004 0.062 6294 Dihedral : 6.865 59.616 5028 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.14 % Allowed : 10.47 % Favored : 88.38 % 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: -0.45 (0.13), residues: 4398 helix: 0.79 (0.14), residues: 1464 sheet: 1.62 (0.25), residues: 408 loop : -1.35 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 551 HIS 0.004 0.001 HIS C 384 PHE 0.010 0.001 PHE E 503 TYR 0.006 0.001 TYR F 244 ARG 0.003 0.000 ARG D 741 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 4.614 Fit side-chains REVERT: A 599 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6604 (mpp-170) REVERT: B 158 MET cc_start: 0.2866 (pmm) cc_final: 0.2415 (pmm) REVERT: C 599 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5731 (mpp-170) REVERT: D 153 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5489 (tm) REVERT: D 158 MET cc_start: 0.2795 (pmm) cc_final: 0.2335 (pmm) REVERT: E 46 MET cc_start: 0.6060 (mmm) cc_final: 0.5549 (mmm) REVERT: E 153 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5230 (tm) REVERT: F 153 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5369 (tm) outliers start: 43 outliers final: 30 residues processed: 164 average time/residue: 0.4245 time to fit residues: 120.3359 Evaluate side-chains 164 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 4.808 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP 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 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG 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 364 ASP Chi-restraints excluded: chain D residue 468 VAL 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 364 ASP Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.0020 chunk 404 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 chunk 236 optimal weight: 50.0000 chunk 171 optimal weight: 7.9990 chunk 308 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 chunk 372 optimal weight: 30.0000 chunk 392 optimal weight: 2.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 35550 Z= 0.430 Angle : 0.619 8.317 48084 Z= 0.301 Chirality : 0.048 0.168 5436 Planarity : 0.004 0.062 6294 Dihedral : 7.144 59.650 5028 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 1.28 % Allowed : 10.47 % Favored : 88.25 % 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: -0.58 (0.13), residues: 4398 helix: 0.60 (0.14), residues: 1470 sheet: 1.40 (0.25), residues: 414 loop : -1.36 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP F 551 HIS 0.004 0.001 HIS A 499 PHE 0.014 0.002 PHE B 363 TYR 0.014 0.001 TYR A 134 ARG 0.015 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 3.887 Fit side-chains REVERT: A 551 TRP cc_start: 0.6478 (t60) cc_final: 0.6152 (t60) REVERT: A 599 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5458 (mpp-170) REVERT: B 158 MET cc_start: 0.2786 (pmm) cc_final: 0.2343 (pmm) REVERT: D 153 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.5353 (tm) REVERT: D 158 MET cc_start: 0.2811 (pmm) cc_final: 0.2342 (pmm) REVERT: E 46 MET cc_start: 0.6105 (mmm) cc_final: 0.5574 (mmm) REVERT: E 153 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5238 (tm) REVERT: F 46 MET cc_start: 0.6310 (mmm) cc_final: 0.6076 (mmm) REVERT: F 153 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5316 (tm) REVERT: F 508 MET cc_start: 0.8714 (mmt) cc_final: 0.8202 (ppp) outliers start: 48 outliers final: 30 residues processed: 166 average time/residue: 0.4248 time to fit residues: 122.0446 Evaluate side-chains 162 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 3.982 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG 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 364 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 10.0000 chunk 415 optimal weight: 0.0070 chunk 253 optimal weight: 0.0170 chunk 197 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35550 Z= 0.155 Angle : 0.488 10.614 48084 Z= 0.234 Chirality : 0.042 0.136 5436 Planarity : 0.004 0.064 6294 Dihedral : 6.786 57.624 5028 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 0.96 % Allowed : 10.71 % Favored : 88.33 % 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: -0.30 (0.13), residues: 4398 helix: 0.97 (0.14), residues: 1458 sheet: 1.81 (0.25), residues: 390 loop : -1.29 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 551 HIS 0.002 0.000 HIS B 226 PHE 0.013 0.001 PHE B 552 TYR 0.008 0.001 TYR F 244 ARG 0.006 0.000 ARG B 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 3.725 Fit side-chains REVERT: A 599 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.5764 (mpp-170) REVERT: B 158 MET cc_start: 0.2799 (pmm) cc_final: 0.2326 (pmm) REVERT: C 599 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.4940 (mpp-170) REVERT: D 153 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5494 (tm) REVERT: D 158 MET cc_start: 0.2703 (pmm) cc_final: 0.2236 (pmm) REVERT: E 46 MET cc_start: 0.6182 (mmm) cc_final: 0.5642 (mmm) REVERT: E 153 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5387 (tm) REVERT: F 46 MET cc_start: 0.6336 (mmm) cc_final: 0.6042 (mmm) REVERT: F 153 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5573 (tm) REVERT: F 599 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5305 (mpp-170) outliers start: 36 outliers final: 21 residues processed: 160 average time/residue: 0.4275 time to fit residues: 117.2579 Evaluate side-chains 158 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 3.580 ------------------------------------------------------------------------------- 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 468 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 599 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 5.9990 chunk 370 optimal weight: 0.0060 chunk 106 optimal weight: 8.9990 chunk 320 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 348 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.124421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074297 restraints weight = 78917.661| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.53 r_work: 0.2683 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35550 Z= 0.199 Angle : 0.498 10.373 48084 Z= 0.237 Chirality : 0.043 0.137 5436 Planarity : 0.004 0.062 6294 Dihedral : 6.706 59.675 5028 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.80 % Allowed : 10.77 % 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: -0.20 (0.13), residues: 4398 helix: 1.06 (0.14), residues: 1452 sheet: 1.76 (0.25), residues: 408 loop : -1.23 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP F 551 HIS 0.002 0.001 HIS F 384 PHE 0.010 0.001 PHE E 503 TYR 0.006 0.001 TYR D 134 ARG 0.003 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5702.05 seconds wall clock time: 105 minutes 20.67 seconds (6320.67 seconds total)