Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 08:16:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/10_2023/3jc5_6535.pdb" } resolution = 4.7 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= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 25340 2.51 5 N 6943 2.21 5 O 7583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 383": "NH1" <-> "NH2" Residue "2 ARG 387": "NH1" <-> "NH2" Residue "2 TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 ARG 534": "NH1" <-> "NH2" Residue "2 ARG 656": "NH1" <-> "NH2" Residue "2 ARG 705": "NH1" <-> "NH2" Residue "2 ARG 794": "NH1" <-> "NH2" Residue "2 ARG 808": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "2 ARG 854": "NH1" <-> "NH2" Residue "2 ARG 859": "NH1" <-> "NH2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 137": "OD1" <-> "OD2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 420": "NH1" <-> "NH2" Residue "3 ARG 435": "NH1" <-> "NH2" Residue "3 ARG 456": "NH1" <-> "NH2" Residue "3 ARG 483": "NH1" <-> "NH2" Residue "3 ARG 509": "NH1" <-> "NH2" Residue "3 ARG 657": "NH1" <-> "NH2" Residue "3 ARG 700": "NH1" <-> "NH2" Residue "3 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 ARG 451": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 557": "NH1" <-> "NH2" Residue "4 ARG 559": "NH1" <-> "NH2" Residue "4 GLU 714": "OE1" <-> "OE2" Residue "4 ARG 796": "NH1" <-> "NH2" Residue "4 ARG 827": "NH1" <-> "NH2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "5 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 152": "OD1" <-> "OD2" Residue "5 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 405": "NH1" <-> "NH2" Residue "5 ARG 407": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "5 ARG 675": "NH1" <-> "NH2" Residue "5 TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 186": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "6 ARG 531": "NH1" <-> "NH2" Residue "6 ARG 691": "NH1" <-> "NH2" Residue "6 ARG 708": "NH1" <-> "NH2" Residue "6 ARG 770": "NH1" <-> "NH2" Residue "6 ARG 781": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 303": "NH1" <-> "NH2" Residue "7 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 400": "NH1" <-> "NH2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 69": "NH1" <-> "NH2" Residue "c ARG 117": "NH1" <-> "NH2" Residue "c PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 226": "NH1" <-> "NH2" Residue "c ARG 307": "NH1" <-> "NH2" Residue "c ARG 398": "NH1" <-> "NH2" Residue "c TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 406": "NH1" <-> "NH2" Residue "c ARG 411": "NH1" <-> "NH2" Residue "c ARG 472": "NH1" <-> "NH2" Residue "c PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 547": "NH1" <-> "NH2" Residue "c TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 587": "NH1" <-> "NH2" Residue "c TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 634": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 40041 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4600 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "3" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4613 Classifications: {'peptide': 588} Link IDs: {'CIS': 20, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 543} Chain breaks: 4 Chain: "4" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4516 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 19, 'PTRANS': 20, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5171 Classifications: {'peptide': 653} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 614} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5211 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 34, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 614} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5148 Classifications: {'peptide': 652} Link IDs: {'CIS': 25, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 597} Chain breaks: 4 Chain: "c" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4470 Classifications: {'peptide': 553} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'CIS': 12, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 165} Chain breaks: 1 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1691 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 20.05, per 1000 atoms: 0.50 Number of scatterers: 40041 At special positions: 0 Unit cell: (168.67, 215.13, 141.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 7583 8.00 N 6943 7.00 C 25340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.72 Conformation dependent library (CDL) restraints added in 5.4 seconds 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9626 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 37 sheets defined 45.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 3.895A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER 2 213 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 253 through 261 removed outlier: 3.919A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.998A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.523A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 removed outlier: 3.601A pdb=" N VAL 2 397 " --> pdb=" O PRO 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '2' and resid 477 through 486 removed outlier: 4.347A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 502 removed outlier: 4.195A pdb=" N ALA 2 502 " --> pdb=" O ILE 2 498 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 3.816A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 2 515 " --> pdb=" O ILE 2 511 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 4.461A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 609 through 612 Processing helix chain '2' and resid 613 through 627 removed outlier: 4.037A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 676 removed outlier: 3.771A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 705 removed outlier: 3.560A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 4.181A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 784 through 799 removed outlier: 3.735A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.048A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.813A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 858 removed outlier: 3.768A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 32 removed outlier: 3.594A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 55 removed outlier: 3.645A pdb=" N ASN 3 49 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 102 through 107 removed outlier: 4.145A pdb=" N PHE 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 3.568A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 135 removed outlier: 3.553A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 removed outlier: 3.538A pdb=" N ALA 3 265 " --> pdb=" O PRO 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 Processing helix chain '3' and resid 344 through 354 removed outlier: 3.785A pdb=" N ARG 3 348 " --> pdb=" O ASP 3 344 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 removed outlier: 3.812A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 491 removed outlier: 3.878A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 543 removed outlier: 3.586A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 569 removed outlier: 3.572A pdb=" N ARG 3 559 " --> pdb=" O GLU 3 555 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER 3 560 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 655 through 666 removed outlier: 3.922A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 675 through 694 removed outlier: 3.527A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.796A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 189 through 196 Processing helix chain '4' and resid 226 through 237 removed outlier: 3.791A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.767A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.660A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 299 removed outlier: 3.571A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 Processing helix chain '4' and resid 478 through 483 removed outlier: 3.729A pdb=" N GLU 4 482 " --> pdb=" O THR 4 478 " (cutoff:3.500A) Processing helix chain '4' and resid 483 through 488 Processing helix chain '4' and resid 502 through 513 removed outlier: 3.928A pdb=" N LEU 4 506 " --> pdb=" O THR 4 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 4 511 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) Processing helix chain '4' and resid 514 through 516 No H-bonds generated for 'chain '4' and resid 514 through 516' Processing helix chain '4' and resid 517 through 527 removed outlier: 3.919A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.555A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.868A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 620 through 624 Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.029A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 692 Processing helix chain '4' and resid 695 through 702 removed outlier: 3.800A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 716 through 725 Processing helix chain '4' and resid 745 through 758 removed outlier: 3.558A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 766 through 779 removed outlier: 3.531A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 821 through 835 removed outlier: 3.617A pdb=" N ALA 4 825 " --> pdb=" O ASP 4 821 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 37 removed outlier: 3.518A pdb=" N SER 5 30 " --> pdb=" O GLU 5 26 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 removed outlier: 4.052A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 72 through 80 removed outlier: 4.166A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 102 Proline residue: 5 88 - end of helix removed outlier: 3.622A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 365 through 371 Processing helix chain '5' and resid 381 through 393 removed outlier: 4.102A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 433 removed outlier: 3.858A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 482 through 485 removed outlier: 3.860A pdb=" N MET 5 485 " --> pdb=" O PHE 5 482 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 482 through 485' Processing helix chain '5' and resid 487 through 500 removed outlier: 3.721A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 5 499 " --> pdb=" O GLU 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 529 through 534 Processing helix chain '5' and resid 544 through 550 Processing helix chain '5' and resid 561 through 577 removed outlier: 3.973A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 582 through 592 removed outlier: 4.096A pdb=" N GLN 5 586 " --> pdb=" O ALA 5 582 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 610 removed outlier: 3.663A pdb=" N LYS 5 600 " --> pdb=" O ILE 5 596 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS 5 610 " --> pdb=" O CYS 5 606 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 637 Processing helix chain '5' and resid 638 through 640 No H-bonds generated for 'chain '5' and resid 638 through 640' Processing helix chain '5' and resid 649 through 668 removed outlier: 3.572A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 3.788A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER 5 693 " --> pdb=" O MET 5 689 " (cutoff:3.500A) Processing helix chain '5' and resid 714 through 719 Processing helix chain '5' and resid 728 through 739 removed outlier: 4.022A pdb=" N ASP 5 739 " --> pdb=" O ARG 5 735 " (cutoff:3.500A) Processing helix chain '5' and resid 744 through 759 Processing helix chain '6' and resid 106 through 121 removed outlier: 3.648A pdb=" N LYS 6 110 " --> pdb=" O VAL 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 144 Processing helix chain '6' and resid 155 through 161 removed outlier: 3.869A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 170 removed outlier: 4.038A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 6 170 " --> pdb=" O LEU 6 166 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 176 Processing helix chain '6' and resid 177 through 193 removed outlier: 3.819A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 511 through 522 removed outlier: 4.191A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 541 through 552 removed outlier: 4.088A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN 6 550 " --> pdb=" O GLY 6 546 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.046A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 644 Processing helix chain '6' and resid 646 through 658 removed outlier: 3.908A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 749 through 759 removed outlier: 3.933A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 783 removed outlier: 3.655A pdb=" N LEU 6 773 " --> pdb=" O ALA 6 769 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS 6 782 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.711A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 837 removed outlier: 3.558A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '6' and resid 908 through 927 removed outlier: 3.598A pdb=" N ARG 6 925 " --> pdb=" O ALA 6 921 " (cutoff:3.500A) Processing helix chain '6' and resid 932 through 945 removed outlier: 3.960A pdb=" N ILE 6 936 " --> pdb=" O THR 6 932 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL 6 937 " --> pdb=" O ALA 6 933 " (cutoff:3.500A) Processing helix chain '6' and resid 950 through 969 removed outlier: 3.515A pdb=" N TYR 6 954 " --> pdb=" O SER 6 950 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 25 removed outlier: 3.757A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.817A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 7 70 " --> pdb=" O MET 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.530A pdb=" N GLN 7 89 " --> pdb=" O ILE 7 85 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN 7 90 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 91 " --> pdb=" O GLN 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.771A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 115 Processing helix chain '7' and resid 119 through 125 removed outlier: 4.025A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 158 removed outlier: 3.599A pdb=" N LEU 7 143 " --> pdb=" O LEU 7 139 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 220 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 397 through 407 removed outlier: 3.633A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 Processing helix chain '7' and resid 425 through 438 removed outlier: 4.095A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 477 Processing helix chain '7' and resid 489 through 494 Processing helix chain '7' and resid 531 through 540 Processing helix chain '7' and resid 541 through 543 No H-bonds generated for 'chain '7' and resid 541 through 543' Processing helix chain '7' and resid 587 through 592 removed outlier: 3.564A pdb=" N LEU 7 591 " --> pdb=" O PRO 7 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER 7 592 " --> pdb=" O ALA 7 588 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 587 through 592' Processing helix chain '7' and resid 605 through 622 removed outlier: 3.762A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 Processing helix chain '7' and resid 653 through 674 removed outlier: 3.507A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.939A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 3.564A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) Processing helix chain '7' and resid 725 through 729 removed outlier: 3.654A pdb=" N TYR 7 728 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 7 729 " --> pdb=" O SER 7 726 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 725 through 729' Processing helix chain 'c' and resid 7 through 18 Processing helix chain 'c' and resid 35 through 52 removed outlier: 3.780A pdb=" N LEU c 39 " --> pdb=" O ASN c 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET c 44 " --> pdb=" O CYS c 40 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 74 removed outlier: 4.203A pdb=" N ARG c 68 " --> pdb=" O TYR c 64 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG c 69 " --> pdb=" O SER c 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 removed outlier: 3.521A pdb=" N PHE c 95 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.930A pdb=" N ILE c 134 " --> pdb=" O ASN c 130 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE c 135 " --> pdb=" O LEU c 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 130 through 135' Processing helix chain 'c' and resid 152 through 157 removed outlier: 3.622A pdb=" N LYS c 156 " --> pdb=" O LEU c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 240 removed outlier: 3.946A pdb=" N VAL c 236 " --> pdb=" O GLU c 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 263 removed outlier: 3.610A pdb=" N GLN c 254 " --> pdb=" O SER c 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA c 261 " --> pdb=" O SER c 257 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE c 262 " --> pdb=" O LEU c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 287 through 289 No H-bonds generated for 'chain 'c' and resid 287 through 289' Processing helix chain 'c' and resid 290 through 301 removed outlier: 4.643A pdb=" N LEU c 294 " --> pdb=" O ARG c 290 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU c 298 " --> pdb=" O LEU c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 340 Processing helix chain 'c' and resid 341 through 348 removed outlier: 3.983A pdb=" N ALA c 346 " --> pdb=" O ASN c 342 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS c 347 " --> pdb=" O TYR c 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 367 removed outlier: 3.752A pdb=" N LYS c 357 " --> pdb=" O GLU c 353 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG c 358 " --> pdb=" O ASN c 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU c 359 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS c 360 " --> pdb=" O LYS c 356 " (cutoff:3.500A) Processing helix chain 'c' and resid 369 through 375 removed outlier: 3.573A pdb=" N GLU c 375 " --> pdb=" O SER c 371 " (cutoff:3.500A) Processing helix chain 'c' and resid 376 through 380 removed outlier: 3.670A pdb=" N MET c 380 " --> pdb=" O TRP c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 381 through 387 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 397 through 400 Processing helix chain 'c' and resid 421 through 434 removed outlier: 3.662A pdb=" N VAL c 425 " --> pdb=" O ALA c 421 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU c 433 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL c 434 " --> pdb=" O ALA c 430 " (cutoff:3.500A) Processing helix chain 'c' and resid 463 through 483 removed outlier: 3.944A pdb=" N TRP c 478 " --> pdb=" O VAL c 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU c 479 " --> pdb=" O SER c 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA c 483 " --> pdb=" O LEU c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 491 through 515 removed outlier: 3.572A pdb=" N LEU c 498 " --> pdb=" O ARG c 494 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP c 501 " --> pdb=" O GLN c 497 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN c 508 " --> pdb=" O ARG c 504 " (cutoff:3.500A) Processing helix chain 'c' and resid 537 through 540 Processing helix chain 'c' and resid 541 through 557 removed outlier: 3.636A pdb=" N ALA c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) Processing helix chain 'c' and resid 604 through 614 removed outlier: 3.588A pdb=" N ILE c 612 " --> pdb=" O ALA c 608 " (cutoff:3.500A) Processing helix chain 'c' and resid 633 through 646 removed outlier: 4.484A pdb=" N SER c 638 " --> pdb=" O ARG c 634 " (cutoff:3.500A) Proline residue: c 639 - end of helix Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 105 removed outlier: 4.027A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 164 removed outlier: 3.640A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 198 Processing helix chain 'D' and resid 279 through 288 removed outlier: 5.006A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.867A pdb=" N GLN B 17 " --> pdb=" O PRO B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.782A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 4.029A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.219A pdb=" N PHE B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.653A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 199 removed outlier: 3.536A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.208A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 removed outlier: 4.021A pdb=" N ASN A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 4.007A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 104 removed outlier: 4.089A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.613A pdb=" N TYR A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 4.034A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.574A pdb=" N VAL C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.706A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 104 through 116 removed outlier: 4.395A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.970A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.743A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.550A pdb=" N PHE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 331 through 333 removed outlier: 3.534A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 331 through 333 removed outlier: 3.534A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 563 through 565 removed outlier: 6.189A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 629 through 631 Processing sheet with id= E, first strand: chain '3' and resid 179 through 180 removed outlier: 7.141A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 210 through 213 Processing sheet with id= G, first strand: chain '3' and resid 391 through 392 removed outlier: 4.016A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 431 through 433 removed outlier: 7.103A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 494 through 497 Processing sheet with id= J, first strand: chain '4' and resid 332 through 335 removed outlier: 6.611A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 339 through 342 Processing sheet with id= L, first strand: chain '4' and resid 344 through 345 Processing sheet with id= M, first strand: chain '4' and resid 365 through 366 removed outlier: 6.902A pdb=" N ILE 4 365 " --> pdb=" O THR 6 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain '4' and resid 434 through 436 removed outlier: 4.197A pdb=" N GLU 4 434 " --> pdb=" O LYS 4 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS 4 467 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 439 through 442 Processing sheet with id= P, first strand: chain '4' and resid 590 through 591 removed outlier: 3.701A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '5' and resid 60 through 63 removed outlier: 6.246A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '5' and resid 298 through 301 removed outlier: 8.913A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 5 292 " --> pdb=" O GLY 5 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '5' and resid 190 through 193 removed outlier: 6.897A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '5' and resid 436 through 440 removed outlier: 3.842A pdb=" N ASP 5 480 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL 5 477 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '6' and resid 150 through 154 removed outlier: 3.674A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '6' and resid 273 through 274 Processing sheet with id= W, first strand: chain '6' and resid 454 through 456 removed outlier: 6.330A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '6' and resid 404 through 405 Processing sheet with id= Y, first strand: chain '6' and resid 570 through 574 removed outlier: 3.579A pdb=" N ILE 6 571 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '6' and resid 660 through 664 Processing sheet with id= AA, first strand: chain '7' and resid 77 through 81 Processing sheet with id= AB, first strand: chain '7' and resid 252 through 253 removed outlier: 6.777A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '7' and resid 252 through 253 removed outlier: 3.587A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '7' and resid 269 through 270 removed outlier: 3.856A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '7' and resid 481 through 483 removed outlier: 6.605A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN 7 455 " --> pdb=" O ILE 7 596 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE 7 598 " --> pdb=" O ASN 7 455 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'c' and resid 119 through 123 removed outlier: 6.946A pdb=" N LEU c 81 " --> pdb=" O TYR c 121 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU c 123 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU c 83 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL c 28 " --> pdb=" O SER c 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE c 58 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 188 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'c' and resid 318 through 321 removed outlier: 5.506A pdb=" N THR c 412 " --> pdb=" O ILE c 419 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE c 419 " --> pdb=" O THR c 412 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY c 414 " --> pdb=" O GLY c 417 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'c' and resid 569 through 571 removed outlier: 3.993A pdb=" N LEU c 569 " --> pdb=" O ALA c 582 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA c 582 " --> pdb=" O LEU c 569 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.021A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 69 through 72 Processing sheet with id= AK, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.607A pdb=" N LEU C 44 " --> pdb=" O CYS C 18 " (cutoff:3.500A) 1486 hydrogen bonds defined for protein. 4272 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: 15.23 Time building geometry restraints manager: 16.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6782 1.30 - 1.44: 10114 1.44 - 1.57: 23482 1.57 - 1.71: 16 1.71 - 1.84: 286 Bond restraints: 40680 Sorted by residual: bond pdb=" N PRO 3 232 " pdb=" CD PRO 3 232 " ideal model delta sigma weight residual 1.473 1.700 -0.227 1.40e-02 5.10e+03 2.63e+02 bond pdb=" C ARG 5 720 " pdb=" N ARG 5 721 " ideal model delta sigma weight residual 1.332 1.173 0.160 1.40e-02 5.10e+03 1.30e+02 bond pdb=" C GLU 6 929 " pdb=" O GLU 6 929 " ideal model delta sigma weight residual 1.235 1.376 -0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C GLN 5 745 " pdb=" N LEU 5 746 " ideal model delta sigma weight residual 1.335 1.451 -0.116 1.36e-02 5.41e+03 7.25e+01 bond pdb=" C GLU 6 930 " pdb=" N LEU 6 931 " ideal model delta sigma weight residual 1.332 1.440 -0.108 1.40e-02 5.10e+03 5.93e+01 ... (remaining 40675 not shown) Histogram of bond angle deviations from ideal: 86.57 - 97.33: 6 97.33 - 108.08: 1881 108.08 - 118.83: 31537 118.83 - 129.59: 21317 129.59 - 140.34: 222 Bond angle restraints: 54963 Sorted by residual: angle pdb=" C THR 5 325 " pdb=" N PRO 5 326 " pdb=" CA PRO 5 326 " ideal model delta sigma weight residual 119.83 140.34 -20.51 1.08e+00 8.57e-01 3.61e+02 angle pdb=" N ARG 5 742 " pdb=" CA ARG 5 742 " pdb=" C ARG 5 742 " ideal model delta sigma weight residual 113.18 134.21 -21.03 1.33e+00 5.65e-01 2.50e+02 angle pdb=" C GLU 4 378 " pdb=" N PRO 4 379 " pdb=" CA PRO 4 379 " ideal model delta sigma weight residual 119.56 134.54 -14.98 1.02e+00 9.61e-01 2.16e+02 angle pdb=" N THR 3 550 " pdb=" CA THR 3 550 " pdb=" C THR 3 550 " ideal model delta sigma weight residual 109.24 86.57 22.67 1.63e+00 3.76e-01 1.93e+02 angle pdb=" C CYS 6 333 " pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " ideal model delta sigma weight residual 119.84 136.29 -16.45 1.25e+00 6.40e-01 1.73e+02 ... (remaining 54958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 24329 26.97 - 53.95: 606 53.95 - 80.92: 63 80.92 - 107.89: 13 107.89 - 134.87: 2 Dihedral angle restraints: 25013 sinusoidal: 10229 harmonic: 14784 Sorted by residual: dihedral pdb=" CA ASN 4 377 " pdb=" C ASN 4 377 " pdb=" N GLU 4 378 " pdb=" CA GLU 4 378 " ideal model delta harmonic sigma weight residual -180.00 -45.13 -134.87 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA GLY 6 600 " pdb=" C GLY 6 600 " pdb=" N LYS 6 601 " pdb=" CA LYS 6 601 " ideal model delta harmonic sigma weight residual 180.00 45.82 134.18 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 122.46 57.54 0 5.00e+00 4.00e-02 1.32e+02 ... (remaining 25010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 6326 0.203 - 0.406: 39 0.406 - 0.609: 2 0.609 - 0.812: 0 0.812 - 1.015: 1 Chirality restraints: 6368 Sorted by residual: chirality pdb=" CA ARG 5 742 " pdb=" N ARG 5 742 " pdb=" C ARG 5 742 " pdb=" CB ARG 5 742 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU 6 931 " pdb=" N LEU 6 931 " pdb=" C LEU 6 931 " pdb=" CB LEU 6 931 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CA GLU 6 929 " pdb=" N GLU 6 929 " pdb=" C GLU 6 929 " pdb=" CB GLU 6 929 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.22e+00 ... (remaining 6365 not shown) Planarity restraints: 7045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 954 " 0.056 2.00e-02 2.50e+03 5.56e-02 6.19e+01 pdb=" CG TYR 6 954 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 954 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 954 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 954 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 954 " -0.053 2.00e-02 2.50e+03 pdb=" CZ TYR 6 954 " -0.054 2.00e-02 2.50e+03 pdb=" OH TYR 6 954 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 6 923 " 0.032 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C VAL 6 923 " -0.111 2.00e-02 2.50e+03 pdb=" O VAL 6 923 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP 6 924 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN 6 943 " 0.032 2.00e-02 2.50e+03 6.28e-02 3.95e+01 pdb=" CD GLN 6 943 " -0.109 2.00e-02 2.50e+03 pdb=" OE1 GLN 6 943 " 0.042 2.00e-02 2.50e+03 pdb=" NE2 GLN 6 943 " 0.035 2.00e-02 2.50e+03 ... (remaining 7042 not shown) Histogram of nonbonded interaction distances: 0.30 - 1.22: 24 1.22 - 2.14: 164 2.14 - 3.06: 29979 3.06 - 3.98: 102399 3.98 - 4.90: 183096 Warning: very small nonbonded interaction distances. Nonbonded interactions: 315662 Sorted by model distance: nonbonded pdb=" NZ LYS 3 391 " pdb=" CG ASN 7 623 " model vdw 0.300 3.350 nonbonded pdb=" CE1 PHE 2 803 " pdb=" NE2 HIS 5 560 " model vdw 0.413 3.420 nonbonded pdb=" O ASN 2 658 " pdb=" CE1 HIS 5 741 " model vdw 0.572 3.260 nonbonded pdb=" CD1 LEU 5 358 " pdb=" NH1 ARG A 15 " model vdw 0.634 3.540 nonbonded pdb=" CD LYS 4 636 " pdb=" CG GLU 7 539 " model vdw 0.692 3.840 ... (remaining 315657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.040 Extract box with map and model: 6.240 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 97.910 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.130 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.009 0.227 40680 Z= 0.606 Angle : 1.544 23.282 54963 Z= 1.004 Chirality : 0.062 1.015 6368 Planarity : 0.006 0.074 7045 Dihedral : 12.175 134.866 15381 Min Nonbonded Distance : 0.300 Molprobity Statistics. All-atom Clashscore : 46.29 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.37 % Favored : 88.93 % Rotamer: Outliers : 0.63 % Allowed : 5.10 % Favored : 94.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 3.46 % Twisted Proline : 0.53 % Twisted General : 0.56 % 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: -4.21 (0.09), residues: 4931 helix: -3.22 (0.08), residues: 1935 sheet: -2.19 (0.17), residues: 594 loop : -2.51 (0.11), residues: 2402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1360 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 1383 average time/residue: 0.5944 time to fit residues: 1271.1441 Evaluate side-chains 719 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 711 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3580 time to fit residues: 12.0614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 421 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 255 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 391 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 453 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 439 ASN ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 2 856 GLN 3 29 GLN 3 239 ASN ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS ** 3 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 ASN 4 184 ASN 4 400 GLN 4 579 GLN 4 646 HIS ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 494 HIS ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN 5 576 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 585 ASN 5 625 ASN 5 758 HIS ** 6 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 ASN 6 570 ASN 6 690 ASN 6 698 ASN 6 735 HIS ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 229 GLN 7 311 GLN 7 384 HIS 7 538 HIS 7 544 GLN 7 585 ASN ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 243 GLN c 249 ASN c 286 GLN c 395 ASN ** c 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 604 ASN ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN B 62 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 188 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 40680 Z= 0.290 Angle : 0.991 14.688 54963 Z= 0.512 Chirality : 0.052 0.397 6368 Planarity : 0.006 0.099 7045 Dihedral : 6.709 73.853 5476 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.15 % Favored : 90.75 % Rotamer: Outliers : 0.54 % Allowed : 4.65 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.53 % Twisted General : 0.25 % 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: -2.73 (0.11), residues: 4931 helix: -1.37 (0.10), residues: 1968 sheet: -1.81 (0.18), residues: 614 loop : -2.15 (0.12), residues: 2349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 937 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 958 average time/residue: 0.5803 time to fit residues: 901.6728 Evaluate side-chains 627 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 625 time to evaluate : 4.787 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3533 time to fit residues: 7.8484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 251 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 308 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 453 optimal weight: 5.9990 chunk 490 optimal weight: 20.0000 chunk 404 optimal weight: 20.0000 chunk 450 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 779 HIS ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 376 HIS ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 522 GLN 3 530 HIS 3 532 ASN 3 569 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN 4 543 GLN 4 757 HIS ** 5 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 581 ASN 5 625 ASN ** 6 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 362 GLN 6 364 ASN ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 237 GLN ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN ** c 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 382 HIS c 395 ASN c 503 GLN c 604 ASN ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 162 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN A 25 GLN ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 40680 Z= 0.266 Angle : 0.896 16.304 54963 Z= 0.464 Chirality : 0.048 0.326 6368 Planarity : 0.005 0.075 7045 Dihedral : 6.280 59.466 5476 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.99 % Allowed : 8.68 % Favored : 90.33 % Rotamer: Outliers : 0.27 % Allowed : 4.85 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.53 % Twisted General : 0.23 % 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: -2.20 (0.11), residues: 4931 helix: -0.73 (0.11), residues: 1988 sheet: -1.85 (0.19), residues: 615 loop : -1.95 (0.12), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 769 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 780 average time/residue: 0.5369 time to fit residues: 681.4145 Evaluate side-chains 555 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 552 time to evaluate : 4.826 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3478 time to fit residues: 8.5946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 448 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 304 optimal weight: 4.9990 chunk 455 optimal weight: 5.9990 chunk 482 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 431 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 432 ASN ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 658 ASN 2 809 HIS 3 46 GLN 3 210 HIS ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 398 HIS 3 493 GLN ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN 4 543 GLN ** 5 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 625 ASN ** 6 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 799 GLN ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS c 57 GLN ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 183 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40680 Z= 0.249 Angle : 0.859 16.851 54963 Z= 0.445 Chirality : 0.048 0.378 6368 Planarity : 0.005 0.178 7045 Dihedral : 6.005 45.839 5476 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.92 % Favored : 90.14 % Rotamer: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.92 (0.11), residues: 4931 helix: -0.37 (0.11), residues: 1999 sheet: -1.76 (0.19), residues: 629 loop : -1.92 (0.13), residues: 2303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 731 time to evaluate : 4.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 735 average time/residue: 0.5290 time to fit residues: 640.0564 Evaluate side-chains 541 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 539 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3330 time to fit residues: 7.2979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 401 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 359 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 411 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 432 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 HIS ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 585 ASN 5 625 ASN ** 6 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 76 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 40680 Z= 0.311 Angle : 0.882 17.592 54963 Z= 0.459 Chirality : 0.048 0.366 6368 Planarity : 0.005 0.070 7045 Dihedral : 5.988 41.620 5476 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.57 % Favored : 89.58 % Rotamer: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.91 (0.11), residues: 4931 helix: -0.30 (0.11), residues: 2006 sheet: -1.76 (0.19), residues: 597 loop : -1.99 (0.12), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 668 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable