Starting phenix.real_space_refine on Sat Dec 16 13:39:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/12_2023/7rl9_24522_updated.pdb" } resolution = 3.3 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= 0.017 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 22098 2.51 5 N 6192 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 304": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F GLU 704": "OE1" <-> "OE2" Residue "F GLU 730": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.82, per 1000 atoms: 0.51 Number of scatterers: 35220 At special positions: 0 Unit cell: (166.402, 181.83, 115.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6726 8.00 N 6192 7.00 C 22098 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.69 Conformation dependent library (CDL) restraints added in 6.7 seconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 18 sheets defined 38.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.862A pdb=" N ARG A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' 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 199 removed outlier: 4.147A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.641A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 458 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: 4.050A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.503A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU A 561 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 565 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 567 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 660 removed outlier: 4.054A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.513A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' 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 199 removed outlier: 4.146A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.565A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.758A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.051A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.503A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.845A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU B 561 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 565 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 567 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 removed outlier: 4.452A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 89' 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 199 removed outlier: 4.147A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 458 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: 4.051A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.672A pdb=" N GLU C 561 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 565 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 567 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 660 removed outlier: 4.053A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.111A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 4.094A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' 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 199 removed outlier: 4.147A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 458 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: 4.051A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU D 561 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 565 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 567 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 660 removed outlier: 4.053A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.511A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' 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 199 removed outlier: 4.147A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 230 No H-bonds generated for 'chain 'E' and resid 227 through 230' Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 458 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: 4.050A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.551A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 565 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 567 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 585 removed outlier: 4.452A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG F 89 " --> pdb=" O ARG F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 89' 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 199 removed outlier: 4.147A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 removed outlier: 3.565A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 458 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: 4.051A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.845A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.551A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU F 561 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS F 565 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 567 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.511A pdb=" N GLU F 689 " --> pdb=" O ALA F 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.111A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12013 1.34 - 1.46: 5005 1.46 - 1.58: 18484 1.58 - 1.69: 30 1.69 - 1.81: 288 Bond restraints: 35820 Sorted by residual: bond pdb=" C4 ADP B1002 " pdb=" C5 ADP B1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C4 ADP D1002 " pdb=" C5 ADP D1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C4 ADP E1002 " pdb=" C5 ADP E1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.76e+00 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.85: 1283 106.85 - 114.08: 20689 114.08 - 121.31: 16869 121.31 - 128.55: 9429 128.55 - 135.78: 162 Bond angle restraints: 48432 Sorted by residual: angle pdb=" N ILE C 32 " pdb=" CA ILE C 32 " pdb=" C ILE C 32 " ideal model delta sigma weight residual 113.71 108.56 5.15 9.50e-01 1.11e+00 2.94e+01 angle pdb=" N ILE A 32 " pdb=" CA ILE A 32 " pdb=" C ILE A 32 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" N ILE E 32 " pdb=" CA ILE E 32 " pdb=" C ILE E 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.90e+01 angle pdb=" N ILE F 32 " pdb=" CA ILE F 32 " pdb=" C ILE F 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.89e+01 angle pdb=" N ILE B 32 " pdb=" CA ILE B 32 " pdb=" C ILE B 32 " ideal model delta sigma weight residual 113.71 108.62 5.09 9.50e-01 1.11e+00 2.87e+01 ... (remaining 48427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 21907 33.32 - 66.63: 207 66.63 - 99.95: 14 99.95 - 133.26: 10 133.26 - 166.58: 8 Dihedral angle restraints: 22146 sinusoidal: 9312 harmonic: 12834 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.58 -166.58 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.10 -166.10 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.65 -160.65 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 22143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3458 0.037 - 0.074: 1465 0.074 - 0.110: 425 0.110 - 0.147: 94 0.147 - 0.184: 6 Chirality restraints: 5448 Sorted by residual: chirality pdb=" CG LEU E 420 " pdb=" CB LEU E 420 " pdb=" CD1 LEU E 420 " pdb=" CD2 LEU E 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU C 420 " pdb=" CB LEU C 420 " pdb=" CD1 LEU C 420 " pdb=" CD2 LEU C 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU D 420 " pdb=" CB LEU D 420 " pdb=" CD1 LEU D 420 " pdb=" CD2 LEU D 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 5445 not shown) Planarity restraints: 6354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS D 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS D 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN D 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C LYS B 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 20 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C LYS A 20 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 6351 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3287 2.75 - 3.29: 35297 3.29 - 3.82: 54136 3.82 - 4.36: 64957 4.36 - 4.90: 106794 Nonbonded interactions: 264471 Sorted by model distance: nonbonded pdb=" O ASP E 669 " pdb=" NH2 ARG E 733 " model vdw 2.210 2.520 nonbonded pdb=" O ASP A 669 " pdb=" NH2 ARG A 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP F 669 " pdb=" NH2 ARG F 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP D 669 " pdb=" NH2 ARG D 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP C 669 " pdb=" NH2 ARG C 733 " model vdw 2.211 2.520 ... (remaining 264466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.940 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 86.710 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.230 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.044 35820 Z= 0.221 Angle : 0.727 10.575 48432 Z= 0.392 Chirality : 0.044 0.184 5448 Planarity : 0.003 0.048 6354 Dihedral : 11.046 166.576 13830 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4440 helix: -0.41 (0.13), residues: 1656 sheet: 0.68 (0.26), residues: 456 loop : -2.28 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 454 HIS 0.002 0.001 HIS D 404 PHE 0.006 0.001 PHE E 773 TYR 0.009 0.001 TYR A 755 ARG 0.009 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4701 time to fit residues: 159.6449 Evaluate side-chains 167 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 4.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 40.0000 chunk 336 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 227 optimal weight: 0.0000 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35820 Z= 0.213 Angle : 0.583 8.233 48432 Z= 0.270 Chirality : 0.044 0.150 5448 Planarity : 0.003 0.043 6354 Dihedral : 9.027 171.370 4962 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.88 % Favored : 91.85 % Rotamer: Outliers : 0.40 % Allowed : 4.38 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4440 helix: -0.33 (0.12), residues: 1728 sheet: 0.76 (0.26), residues: 456 loop : -2.05 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 454 HIS 0.004 0.001 HIS F 340 PHE 0.013 0.001 PHE F 773 TYR 0.010 0.001 TYR B 517 ARG 0.003 0.000 ARG E 635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 199 average time/residue: 0.4309 time to fit residues: 150.6292 Evaluate side-chains 196 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 4.364 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3232 time to fit residues: 12.5081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 335 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 400 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 324 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 ASN C 351 ASN F 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35820 Z= 0.183 Angle : 0.547 9.067 48432 Z= 0.250 Chirality : 0.043 0.137 5448 Planarity : 0.003 0.043 6354 Dihedral : 8.577 159.730 4962 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.09 % Favored : 92.64 % Rotamer: Outliers : 0.53 % Allowed : 5.64 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4440 helix: -0.07 (0.13), residues: 1752 sheet: 0.90 (0.26), residues: 456 loop : -1.88 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 454 HIS 0.003 0.001 HIS F 340 PHE 0.016 0.001 PHE F 265 TYR 0.008 0.001 TYR A 517 ARG 0.003 0.000 ARG C 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 200 average time/residue: 0.4187 time to fit residues: 146.7055 Evaluate side-chains 181 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 3.897 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3255 time to fit residues: 7.9751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.7980 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 405 optimal weight: 4.9990 chunk 429 optimal weight: 1.9990 chunk 211 optimal weight: 0.1980 chunk 384 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 616 ASN E 348 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35820 Z= 0.278 Angle : 0.596 8.801 48432 Z= 0.278 Chirality : 0.045 0.155 5448 Planarity : 0.003 0.043 6354 Dihedral : 8.517 177.599 4962 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 1.42 % Allowed : 6.49 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4440 helix: 0.10 (0.13), residues: 1716 sheet: 0.92 (0.26), residues: 456 loop : -1.76 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 454 HIS 0.005 0.001 HIS F 226 PHE 0.018 0.002 PHE C 290 TYR 0.013 0.002 TYR C 244 ARG 0.005 0.000 ARG E 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 4.341 Fit side-chains outliers start: 54 outliers final: 25 residues processed: 200 average time/residue: 0.4306 time to fit residues: 150.9079 Evaluate side-chains 188 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 4.136 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3354 time to fit residues: 21.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 6 optimal weight: 50.0000 chunk 319 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 1.9990 chunk 296 optimal weight: 60.0000 chunk 0 optimal weight: 50.0000 chunk 219 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS B 406 HIS C 406 HIS E 406 HIS F 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35820 Z= 0.226 Angle : 0.556 7.084 48432 Z= 0.255 Chirality : 0.044 0.157 5448 Planarity : 0.003 0.044 6354 Dihedral : 7.842 159.292 4962 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.61 % Favored : 92.25 % Rotamer: Outliers : 0.92 % Allowed : 6.86 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4440 helix: 0.17 (0.13), residues: 1752 sheet: 0.96 (0.26), residues: 456 loop : -1.73 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 454 HIS 0.004 0.001 HIS F 340 PHE 0.012 0.001 PHE E 290 TYR 0.011 0.001 TYR A 244 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 193 average time/residue: 0.4180 time to fit residues: 143.2510 Evaluate side-chains 179 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 3.941 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3127 time to fit residues: 19.4200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 7.9990 chunk 386 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 429 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 40.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35820 Z= 0.382 Angle : 0.646 8.301 48432 Z= 0.306 Chirality : 0.046 0.132 5448 Planarity : 0.004 0.046 6354 Dihedral : 7.318 162.626 4962 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 1.00 % Allowed : 8.15 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4440 helix: -0.09 (0.12), residues: 1818 sheet: 0.89 (0.26), residues: 456 loop : -1.76 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 454 HIS 0.005 0.001 HIS F 340 PHE 0.019 0.002 PHE C 290 TYR 0.024 0.002 TYR E 244 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 4.072 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 184 average time/residue: 0.4515 time to fit residues: 147.8480 Evaluate side-chains 171 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 4.184 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3368 time to fit residues: 18.8415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 chunk 313 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 427 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35820 Z= 0.212 Angle : 0.577 10.121 48432 Z= 0.266 Chirality : 0.044 0.153 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.927 162.264 4962 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 0.63 % Allowed : 8.49 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4440 helix: 0.12 (0.12), residues: 1818 sheet: 1.00 (0.26), residues: 438 loop : -1.72 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 454 HIS 0.005 0.001 HIS C 340 PHE 0.016 0.001 PHE D 363 TYR 0.010 0.001 TYR A 244 ARG 0.004 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 3.907 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 178 average time/residue: 0.4289 time to fit residues: 134.0785 Evaluate side-chains 169 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3145 time to fit residues: 14.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 0.0370 chunk 211 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN B 384 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35820 Z= 0.190 Angle : 0.559 12.173 48432 Z= 0.256 Chirality : 0.044 0.149 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.662 163.106 4962 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 0.37 % Allowed : 9.41 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4440 helix: 0.29 (0.13), residues: 1788 sheet: 1.08 (0.26), residues: 438 loop : -1.65 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 454 HIS 0.005 0.001 HIS D 340 PHE 0.016 0.001 PHE A 363 TYR 0.016 0.001 TYR A 244 ARG 0.005 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 4.151 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 169 average time/residue: 0.4528 time to fit residues: 133.6915 Evaluate side-chains 155 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3534 time to fit residues: 9.0134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.3980 chunk 409 optimal weight: 7.9990 chunk 374 optimal weight: 7.9990 chunk 398 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 360 optimal weight: 5.9990 chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: