Starting phenix.real_space_refine on Sun Mar 24 05:00:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/03_2024/3jc5_6535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/03_2024/3jc5_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_6535/03_2024/3jc5_6535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/03_2024/3jc5_6535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/03_2024/3jc5_6535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc5_6535/03_2024/3jc5_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 20.21, 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: 15.70 Conformation dependent library (CDL) restraints added in 6.8 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: 4.23 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: 15.44 Time building geometry restraints manager: 16.93 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: 0.820 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: 6.150 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 101.010 Find NCS groups from input model: 1.990 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.820 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP 6 939 HIS 0.028 0.002 HIS 5 758 PHE 0.041 0.003 PHE 5 743 TYR 0.113 0.003 TYR 6 954 ARG 0.034 0.001 ARG 6 958 *********************** 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 : 4.068 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 REVERT: 2 221 GLU cc_start: 0.9015 (mp0) cc_final: 0.8641 (mp0) REVERT: 2 258 LEU cc_start: 0.9313 (tp) cc_final: 0.9088 (mm) REVERT: 2 265 GLU cc_start: 0.9347 (tp30) cc_final: 0.9118 (tp30) REVERT: 2 292 GLU cc_start: 0.9693 (tp30) cc_final: 0.9299 (tm-30) REVERT: 2 456 ILE cc_start: 0.9349 (mm) cc_final: 0.9007 (mm) REVERT: 2 537 ILE cc_start: 0.7481 (mp) cc_final: 0.6952 (mm) REVERT: 2 596 LEU cc_start: 0.8337 (mt) cc_final: 0.7887 (mm) REVERT: 2 612 MET cc_start: 0.6213 (mtp) cc_final: 0.5203 (ttp) REVERT: 2 780 GLN cc_start: 0.5241 (tt0) cc_final: 0.4986 (mm-40) REVERT: 2 816 ILE cc_start: 0.9000 (mt) cc_final: 0.8710 (tp) REVERT: 3 100 LEU cc_start: 0.9307 (mt) cc_final: 0.9089 (mp) REVERT: 3 260 GLU cc_start: 0.8284 (pm20) cc_final: 0.7931 (tm-30) REVERT: 3 278 LEU cc_start: 0.8858 (mt) cc_final: 0.8411 (mt) REVERT: 3 472 ILE cc_start: 0.7687 (mt) cc_final: 0.7435 (mp) REVERT: 3 683 TYR cc_start: 0.6152 (t80) cc_final: 0.5474 (t80) REVERT: 3 706 ILE cc_start: 0.7944 (pt) cc_final: 0.7629 (pt) REVERT: 4 262 LEU cc_start: 0.9263 (tp) cc_final: 0.8983 (mt) REVERT: 4 328 LEU cc_start: 0.8871 (mt) cc_final: 0.8583 (mt) REVERT: 4 329 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7704 (tmtt) REVERT: 4 382 MET cc_start: 0.8344 (tpp) cc_final: 0.7701 (mmp) REVERT: 4 486 MET cc_start: -0.0670 (mtt) cc_final: -0.1077 (ttt) REVERT: 4 637 MET cc_start: -0.1155 (mmt) cc_final: -0.3206 (ttt) REVERT: 5 41 ASP cc_start: 0.9274 (m-30) cc_final: 0.8609 (t0) REVERT: 5 55 LEU cc_start: 0.9614 (mt) cc_final: 0.8639 (tp) REVERT: 5 68 LEU cc_start: 0.9716 (tt) cc_final: 0.9408 (tt) REVERT: 5 75 ILE cc_start: 0.9536 (pt) cc_final: 0.9244 (pt) REVERT: 5 76 TYR cc_start: 0.9065 (t80) cc_final: 0.8745 (t80) REVERT: 5 169 THR cc_start: 0.8447 (p) cc_final: 0.8195 (p) REVERT: 5 181 ILE cc_start: 0.8720 (mt) cc_final: 0.8029 (mm) REVERT: 5 242 ILE cc_start: 0.9395 (mt) cc_final: 0.9119 (tp) REVERT: 5 275 THR cc_start: 0.8756 (m) cc_final: 0.8120 (p) REVERT: 5 281 TYR cc_start: 0.8683 (m-80) cc_final: 0.8316 (m-80) REVERT: 5 285 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8961 (mtpp) REVERT: 5 298 TYR cc_start: 0.8917 (t80) cc_final: 0.8697 (t80) REVERT: 5 357 PHE cc_start: 0.8008 (m-10) cc_final: 0.7144 (m-80) REVERT: 5 391 LEU cc_start: 0.8804 (tt) cc_final: 0.8475 (tt) REVERT: 5 583 MET cc_start: 0.0725 (OUTLIER) cc_final: -0.0425 (ptt) REVERT: 6 178 LEU cc_start: 0.9435 (mp) cc_final: 0.9129 (tp) REVERT: 6 270 LEU cc_start: 0.9340 (mt) cc_final: 0.8888 (tt) REVERT: 6 287 LEU cc_start: 0.8515 (mp) cc_final: 0.7851 (pt) REVERT: 6 359 VAL cc_start: 0.9114 (m) cc_final: 0.8819 (m) REVERT: 6 628 LEU cc_start: 0.8213 (tt) cc_final: 0.7892 (tp) REVERT: 7 14 TYR cc_start: 0.8422 (m-80) cc_final: 0.7040 (m-80) REVERT: 7 66 MET cc_start: 0.9072 (ttp) cc_final: 0.8781 (tpp) REVERT: 7 116 LEU cc_start: 0.9363 (tt) cc_final: 0.9008 (mt) REVERT: 7 202 LEU cc_start: 0.9606 (tt) cc_final: 0.9336 (tt) REVERT: 7 211 CYS cc_start: 0.7255 (p) cc_final: 0.6722 (t) REVERT: 7 235 LEU cc_start: 0.8338 (mt) cc_final: 0.7894 (mm) REVERT: 7 260 TYR cc_start: 0.6551 (p90) cc_final: 0.6338 (p90) REVERT: 7 457 CYS cc_start: 0.7345 (t) cc_final: 0.5462 (t) REVERT: 7 540 VAL cc_start: 0.7730 (t) cc_final: 0.7213 (m) REVERT: c 297 ASP cc_start: 0.9472 (m-30) cc_final: 0.9252 (p0) REVERT: c 361 LYS cc_start: 0.9479 (ttmt) cc_final: 0.9269 (tttm) REVERT: c 375 GLU cc_start: 0.9303 (tt0) cc_final: 0.8925 (pt0) REVERT: c 391 ILE cc_start: 0.9560 (mt) cc_final: 0.8872 (tp) REVERT: c 413 LEU cc_start: 0.7330 (tp) cc_final: 0.6895 (mt) REVERT: c 469 LEU cc_start: 0.9277 (tt) cc_final: 0.8857 (pp) REVERT: c 524 ILE cc_start: 0.6959 (mt) cc_final: 0.6401 (mt) REVERT: c 576 THR cc_start: 0.7707 (p) cc_final: 0.7464 (t) REVERT: c 607 MET cc_start: 0.9154 (mtp) cc_final: 0.8725 (mpp) REVERT: D 67 TRP cc_start: 0.9059 (t60) cc_final: 0.8724 (t60) REVERT: D 133 LEU cc_start: 0.9258 (tt) cc_final: 0.8901 (pp) REVERT: D 148 LEU cc_start: 0.9695 (mt) cc_final: 0.9475 (pp) REVERT: D 200 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8993 (mttt) REVERT: D 256 TYR cc_start: 0.7845 (p90) cc_final: 0.7297 (p90) REVERT: B 19 ILE cc_start: 0.9157 (mt) cc_final: 0.8817 (mp) REVERT: B 53 ILE cc_start: 0.8772 (mp) cc_final: 0.8499 (pt) REVERT: B 74 TRP cc_start: 0.9149 (p-90) cc_final: 0.7854 (p-90) REVERT: B 104 TYR cc_start: 0.9104 (t80) cc_final: 0.8765 (t80) REVERT: B 119 TRP cc_start: 0.8653 (p-90) cc_final: 0.8210 (p-90) REVERT: B 132 ASP cc_start: 0.9506 (p0) cc_final: 0.9205 (p0) REVERT: B 138 ILE cc_start: 0.9054 (pt) cc_final: 0.8853 (pt) REVERT: B 145 ILE cc_start: 0.9074 (pp) cc_final: 0.8780 (pp) REVERT: B 147 ASP cc_start: 0.9514 (t0) cc_final: 0.9176 (t0) REVERT: B 155 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8759 (ttmt) REVERT: B 177 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8909 (mt-10) REVERT: B 186 THR cc_start: 0.9387 (p) cc_final: 0.9070 (t) REVERT: A 2 TYR cc_start: 0.6881 (t80) cc_final: 0.6247 (t80) REVERT: A 24 ASN cc_start: 0.8901 (t0) cc_final: 0.8479 (m-40) REVERT: A 176 THR cc_start: 0.8117 (m) cc_final: 0.7817 (p) REVERT: C 12 ASP cc_start: 0.9392 (m-30) cc_final: 0.9014 (m-30) REVERT: C 96 ASP cc_start: 0.9148 (t0) cc_final: 0.8907 (t0) REVERT: C 126 GLU cc_start: 0.9400 (tp30) cc_final: 0.9178 (mm-30) REVERT: C 134 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8730 (tm-30) outliers start: 28 outliers final: 8 residues processed: 1383 average time/residue: 0.5887 time to fit residues: 1263.2360 Evaluate side-chains 749 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 740 time to evaluate : 4.690 ------------------------------------------------------------------------------- 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: 0.2980 chunk 129 optimal weight: 0.7980 chunk 255 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 391 optimal weight: 0.4980 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: 0.7184 ------------------------------------------------------------------------------- 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** 2 432 ASN 2 439 ASN ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 2 856 GLN 3 29 GLN ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN 3 688 ASN 4 184 ASN 4 400 GLN ** 4 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 494 HIS 5 574 ASN 5 576 HIS ** 5 579 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 550 ASN c 604 ASN ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS 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 Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 40680 Z= 0.291 Angle : 0.992 15.492 54963 Z= 0.512 Chirality : 0.051 0.447 6368 Planarity : 0.006 0.108 7045 Dihedral : 6.703 74.144 5476 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.48 % Favored : 90.43 % Rotamer: Outliers : 0.49 % Allowed : 4.52 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 3.71 % Twisted Proline : 1.60 % 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: -2.76 (0.11), residues: 4931 helix: -1.40 (0.10), residues: 1973 sheet: -1.86 (0.18), residues: 612 loop : -2.16 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 478 HIS 0.014 0.002 HIS 6 653 PHE 0.049 0.002 PHE 2 803 TYR 0.035 0.002 TYR 4 519 ARG 0.015 0.001 ARG c 290 *********************** 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 986 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 964 time to evaluate : 4.967 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: 2 258 LEU cc_start: 0.9388 (tp) cc_final: 0.9159 (mm) REVERT: 2 266 GLU cc_start: 0.8600 (pm20) cc_final: 0.8038 (pp20) REVERT: 2 267 MET cc_start: 0.8885 (ppp) cc_final: 0.8426 (ppp) REVERT: 2 274 VAL cc_start: 0.9271 (t) cc_final: 0.8921 (t) REVERT: 2 293 ILE cc_start: 0.9723 (mp) cc_final: 0.9337 (tt) REVERT: 2 334 LEU cc_start: 0.9382 (tp) cc_final: 0.9168 (pt) REVERT: 2 415 VAL cc_start: 0.8804 (t) cc_final: 0.8301 (t) REVERT: 2 537 ILE cc_start: 0.7471 (mp) cc_final: 0.7039 (mm) REVERT: 2 596 LEU cc_start: 0.7897 (mt) cc_final: 0.7417 (mm) REVERT: 2 651 ASN cc_start: 0.8131 (p0) cc_final: 0.7594 (p0) REVERT: 3 167 SER cc_start: 0.9350 (p) cc_final: 0.8941 (t) REVERT: 3 205 LYS cc_start: 0.9235 (mppt) cc_final: 0.8595 (tptt) REVERT: 3 260 GLU cc_start: 0.8337 (pm20) cc_final: 0.7828 (tm-30) REVERT: 3 261 MET cc_start: 0.8533 (mmm) cc_final: 0.7615 (mmm) REVERT: 3 278 LEU cc_start: 0.8985 (mt) cc_final: 0.8487 (mt) REVERT: 3 292 VAL cc_start: 0.9116 (t) cc_final: 0.8681 (p) REVERT: 3 416 SER cc_start: 0.8046 (p) cc_final: 0.7427 (p) REVERT: 3 480 ASP cc_start: 0.8262 (m-30) cc_final: 0.7140 (m-30) REVERT: 3 665 GLU cc_start: 0.4483 (OUTLIER) cc_final: 0.4242 (pp20) REVERT: 4 293 LEU cc_start: 0.7741 (tp) cc_final: 0.7049 (pt) REVERT: 4 322 ILE cc_start: 0.8635 (pt) cc_final: 0.8263 (mp) REVERT: 4 382 MET cc_start: 0.8369 (tpp) cc_final: 0.7793 (mmp) REVERT: 4 439 PHE cc_start: 0.9304 (t80) cc_final: 0.9079 (t80) REVERT: 4 486 MET cc_start: -0.0356 (mtt) cc_final: -0.0887 (ttt) REVERT: 4 637 MET cc_start: -0.3453 (mmt) cc_final: -0.4761 (ttm) REVERT: 5 32 LYS cc_start: 0.9503 (mttt) cc_final: 0.9146 (mttm) REVERT: 5 55 LEU cc_start: 0.9278 (mt) cc_final: 0.8858 (tp) REVERT: 5 59 TYR cc_start: 0.8426 (m-80) cc_final: 0.8174 (m-80) REVERT: 5 76 TYR cc_start: 0.8811 (t80) cc_final: 0.8608 (t80) REVERT: 5 99 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9021 (mmmt) REVERT: 5 132 LEU cc_start: 0.9060 (mt) cc_final: 0.8751 (mt) REVERT: 5 148 LEU cc_start: 0.9412 (tt) cc_final: 0.9178 (tt) REVERT: 5 252 ASP cc_start: 0.8055 (t0) cc_final: 0.7659 (t0) REVERT: 5 497 MET cc_start: 0.7953 (ptm) cc_final: 0.7470 (ppp) REVERT: 5 583 MET cc_start: 0.1757 (mmp) cc_final: -0.0997 (ptt) REVERT: 6 160 MET cc_start: 0.8829 (ptt) cc_final: 0.8343 (ptp) REVERT: 6 168 MET cc_start: 0.8697 (mmp) cc_final: 0.8336 (mmp) REVERT: 6 270 LEU cc_start: 0.9334 (mt) cc_final: 0.8926 (tt) REVERT: 6 287 LEU cc_start: 0.8360 (mp) cc_final: 0.7720 (pt) REVERT: 6 377 LEU cc_start: 0.8885 (tt) cc_final: 0.8595 (mt) REVERT: 6 378 ASP cc_start: 0.9200 (m-30) cc_final: 0.8784 (m-30) REVERT: 6 525 ILE cc_start: 0.7689 (pt) cc_final: 0.6786 (pt) REVERT: 6 569 ILE cc_start: 0.8498 (tp) cc_final: 0.7893 (tp) REVERT: 6 652 ILE cc_start: 0.9532 (mp) cc_final: 0.9068 (tp) REVERT: 7 14 TYR cc_start: 0.8166 (m-80) cc_final: 0.6774 (m-80) REVERT: 7 29 LYS cc_start: 0.8044 (tptt) cc_final: 0.7673 (tmtt) REVERT: 7 66 MET cc_start: 0.9157 (ttp) cc_final: 0.8915 (tpp) REVERT: 7 235 LEU cc_start: 0.8503 (mt) cc_final: 0.8193 (mt) REVERT: 7 307 PHE cc_start: 0.7477 (m-80) cc_final: 0.7076 (m-10) REVERT: c 44 MET cc_start: 0.8861 (ptt) cc_final: 0.8271 (ptt) REVERT: c 45 LEU cc_start: 0.9632 (tp) cc_final: 0.9261 (tp) REVERT: c 49 PHE cc_start: 0.8866 (m-10) cc_final: 0.8355 (m-80) REVERT: c 81 LEU cc_start: 0.9132 (tt) cc_final: 0.8842 (tt) REVERT: c 297 ASP cc_start: 0.9364 (m-30) cc_final: 0.9027 (p0) REVERT: c 334 LEU cc_start: 0.9363 (tp) cc_final: 0.9135 (tp) REVERT: c 391 ILE cc_start: 0.9508 (mt) cc_final: 0.9160 (tp) REVERT: c 413 LEU cc_start: 0.6707 (tp) cc_final: 0.6409 (mt) REVERT: c 469 LEU cc_start: 0.9242 (tt) cc_final: 0.8875 (pp) REVERT: c 493 ASN cc_start: 0.9026 (m-40) cc_final: 0.8791 (p0) REVERT: c 558 GLU cc_start: 0.8258 (mp0) cc_final: 0.7625 (tp30) REVERT: D 64 MET cc_start: 0.8922 (mmp) cc_final: 0.8600 (mmm) REVERT: D 148 LEU cc_start: 0.9662 (mt) cc_final: 0.9371 (pp) REVERT: D 156 LEU cc_start: 0.9452 (mt) cc_final: 0.9100 (tp) REVERT: D 200 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9063 (mtmm) REVERT: D 202 MET cc_start: 0.8810 (tpp) cc_final: 0.8505 (tpp) REVERT: D 227 PHE cc_start: 0.7852 (m-80) cc_final: 0.7562 (m-80) REVERT: B 9 GLN cc_start: 0.9439 (mm110) cc_final: 0.9210 (mm110) REVERT: B 75 ILE cc_start: 0.9677 (pt) cc_final: 0.9410 (mm) REVERT: B 99 ASP cc_start: 0.9115 (m-30) cc_final: 0.8908 (m-30) REVERT: B 110 ASP cc_start: 0.9365 (p0) cc_final: 0.8421 (t0) REVERT: B 119 TRP cc_start: 0.8323 (p-90) cc_final: 0.7792 (p-90) REVERT: B 132 ASP cc_start: 0.9507 (p0) cc_final: 0.9140 (p0) REVERT: B 142 ARG cc_start: 0.8374 (ptp-110) cc_final: 0.7486 (tpp80) REVERT: B 156 VAL cc_start: 0.9322 (t) cc_final: 0.9090 (t) REVERT: B 177 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8969 (mt-10) REVERT: B 195 ILE cc_start: 0.9146 (pt) cc_final: 0.8905 (pt) REVERT: A 24 ASN cc_start: 0.8834 (t0) cc_final: 0.8569 (m-40) REVERT: A 38 ARG cc_start: 0.9383 (ttm110) cc_final: 0.9045 (tpp-160) REVERT: A 110 MET cc_start: 0.0795 (tpt) cc_final: 0.0335 (tpt) REVERT: C 10 LEU cc_start: 0.9469 (tp) cc_final: 0.9241 (tp) REVERT: C 20 PHE cc_start: 0.8783 (m-80) cc_final: 0.8012 (m-80) REVERT: C 24 ILE cc_start: 0.8595 (mp) cc_final: 0.8336 (mm) REVERT: C 44 LEU cc_start: 0.9198 (tp) cc_final: 0.8964 (mm) REVERT: C 126 GLU cc_start: 0.9454 (tp30) cc_final: 0.9230 (mm-30) REVERT: C 191 MET cc_start: 0.8320 (tpt) cc_final: 0.7973 (tpp) outliers start: 22 outliers final: 1 residues processed: 984 average time/residue: 0.5376 time to fit residues: 855.0343 Evaluate side-chains 673 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 671 time to evaluate : 3.886 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 6.9990 chunk 377 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 453 optimal weight: 7.9990 chunk 490 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 450 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 364 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 46 GLN 3 210 HIS 3 239 ASN ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 376 HIS 3 417 GLN ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN 4 543 GLN 4 579 GLN 4 757 HIS ** 5 411 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 76 ASN 7 538 HIS ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN ** c 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 395 ASN c 503 GLN c 604 ASN ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 40680 Z= 0.344 Angle : 0.924 18.401 54963 Z= 0.483 Chirality : 0.049 0.323 6368 Planarity : 0.006 0.078 7045 Dihedral : 6.350 57.381 5476 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.04 % Favored : 89.96 % Rotamer: Outliers : 0.31 % Allowed : 5.06 % Favored : 94.63 % 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: -2.19 (0.11), residues: 4931 helix: -0.69 (0.11), residues: 1999 sheet: -1.87 (0.18), residues: 641 loop : -1.98 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 478 HIS 0.033 0.002 HIS 5 741 PHE 0.028 0.002 PHE 5 357 TYR 0.031 0.002 TYR 6 621 ARG 0.027 0.001 ARG 3 483 *********************** 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 770 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 756 time to evaluate : 4.961 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: 2 258 LEU cc_start: 0.9428 (tp) cc_final: 0.9167 (mm) REVERT: 2 266 GLU cc_start: 0.8801 (pm20) cc_final: 0.8284 (pm20) REVERT: 2 267 MET cc_start: 0.8817 (ppp) cc_final: 0.8282 (ppp) REVERT: 2 537 ILE cc_start: 0.7731 (mp) cc_final: 0.7379 (mm) REVERT: 2 558 LYS cc_start: 0.8563 (pttm) cc_final: 0.8302 (pptt) REVERT: 2 609 PHE cc_start: 0.6955 (m-10) cc_final: 0.6494 (m-10) REVERT: 2 612 MET cc_start: 0.7623 (ptt) cc_final: 0.6889 (ttp) REVERT: 2 616 ASP cc_start: 0.7580 (t70) cc_final: 0.7297 (t70) REVERT: 2 620 ILE cc_start: 0.8952 (mt) cc_final: 0.8673 (mt) REVERT: 3 176 LEU cc_start: 0.8841 (tt) cc_final: 0.8632 (tt) REVERT: 3 205 LYS cc_start: 0.9267 (mppt) cc_final: 0.8716 (tptt) REVERT: 3 260 GLU cc_start: 0.8423 (pm20) cc_final: 0.8025 (tm-30) REVERT: 3 278 LEU cc_start: 0.9079 (mt) cc_final: 0.8646 (mt) REVERT: 3 282 LEU cc_start: 0.9570 (mt) cc_final: 0.9264 (mt) REVERT: 3 375 ASP cc_start: 0.7639 (t0) cc_final: 0.7342 (t0) REVERT: 3 480 ASP cc_start: 0.8544 (m-30) cc_final: 0.8311 (m-30) REVERT: 4 293 LEU cc_start: 0.8091 (tp) cc_final: 0.7336 (pt) REVERT: 4 382 MET cc_start: 0.8368 (tpp) cc_final: 0.7990 (mmp) REVERT: 4 391 PHE cc_start: 0.8708 (m-80) cc_final: 0.8190 (m-80) REVERT: 4 486 MET cc_start: 0.0614 (mtt) cc_final: -0.0063 (ttt) REVERT: 4 637 MET cc_start: -0.3556 (mmt) cc_final: -0.4830 (ttm) REVERT: 4 801 MET cc_start: 0.1352 (tpt) cc_final: 0.0471 (tpt) REVERT: 5 32 LYS cc_start: 0.9533 (mttt) cc_final: 0.9059 (mmmt) REVERT: 5 48 ASP cc_start: 0.9219 (m-30) cc_final: 0.9003 (p0) REVERT: 5 55 LEU cc_start: 0.9355 (mt) cc_final: 0.8822 (tp) REVERT: 5 58 ASN cc_start: 0.9125 (t0) cc_final: 0.8920 (t0) REVERT: 5 497 MET cc_start: 0.7887 (ppp) cc_final: 0.7617 (ppp) REVERT: 5 583 MET cc_start: 0.1539 (mmp) cc_final: -0.1498 (ptt) REVERT: 5 598 LYS cc_start: 0.9352 (mmpt) cc_final: 0.9141 (mmmt) REVERT: 6 160 MET cc_start: 0.8980 (ptt) cc_final: 0.8418 (ptp) REVERT: 6 262 VAL cc_start: 0.8968 (m) cc_final: 0.8507 (t) REVERT: 6 270 LEU cc_start: 0.9406 (mt) cc_final: 0.9056 (tp) REVERT: 6 287 LEU cc_start: 0.8542 (mp) cc_final: 0.7780 (pt) REVERT: 6 377 LEU cc_start: 0.8910 (tt) cc_final: 0.8448 (mt) REVERT: 6 378 ASP cc_start: 0.9184 (m-30) cc_final: 0.8770 (m-30) REVERT: 7 14 TYR cc_start: 0.8132 (m-80) cc_final: 0.7463 (m-80) REVERT: 7 29 LYS cc_start: 0.8103 (tptt) cc_final: 0.7716 (tmtt) REVERT: 7 620 HIS cc_start: 0.6661 (p-80) cc_final: 0.6162 (p-80) REVERT: c 45 LEU cc_start: 0.9629 (tp) cc_final: 0.9170 (tp) REVERT: c 49 PHE cc_start: 0.9038 (m-10) cc_final: 0.8442 (m-80) REVERT: c 297 ASP cc_start: 0.9377 (m-30) cc_final: 0.9130 (p0) REVERT: c 413 LEU cc_start: 0.7269 (tp) cc_final: 0.6994 (mt) REVERT: c 524 ILE cc_start: 0.6864 (mt) cc_final: 0.6566 (mt) REVERT: c 547 ARG cc_start: 0.9282 (ptm160) cc_final: 0.9055 (ptm160) REVERT: c 558 GLU cc_start: 0.7716 (mp0) cc_final: 0.7403 (tp30) REVERT: c 569 LEU cc_start: 0.9426 (mt) cc_final: 0.9155 (mt) REVERT: D 64 MET cc_start: 0.9101 (mmp) cc_final: 0.8779 (mmm) REVERT: D 134 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9275 (mm-30) REVERT: D 148 LEU cc_start: 0.9760 (mt) cc_final: 0.9344 (pp) REVERT: D 156 LEU cc_start: 0.9494 (mt) cc_final: 0.9112 (tp) REVERT: D 200 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9202 (mtmm) REVERT: D 202 MET cc_start: 0.9001 (tpp) cc_final: 0.8567 (tpp) REVERT: D 227 PHE cc_start: 0.7900 (m-80) cc_final: 0.7637 (m-80) REVERT: D 277 MET cc_start: 0.8171 (mmt) cc_final: 0.7849 (mmp) REVERT: B 74 TRP cc_start: 0.8946 (p-90) cc_final: 0.8508 (p-90) REVERT: B 110 ASP cc_start: 0.9471 (p0) cc_final: 0.8365 (t0) REVERT: B 119 TRP cc_start: 0.8413 (p-90) cc_final: 0.7778 (p-90) REVERT: B 132 ASP cc_start: 0.9614 (p0) cc_final: 0.9352 (p0) REVERT: B 177 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9066 (mt-10) REVERT: A 24 ASN cc_start: 0.8800 (t0) cc_final: 0.8574 (m-40) REVERT: A 110 MET cc_start: 0.0274 (tpt) cc_final: -0.0313 (tpp) REVERT: A 189 PHE cc_start: 0.9080 (m-80) cc_final: 0.8847 (m-10) REVERT: A 198 ARG cc_start: 0.6742 (ptp-170) cc_final: 0.6412 (ptp-170) REVERT: C 20 PHE cc_start: 0.8936 (m-80) cc_final: 0.8478 (m-80) REVERT: C 52 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8577 (tpp80) REVERT: C 96 ASP cc_start: 0.9497 (t0) cc_final: 0.9164 (t0) REVERT: C 126 GLU cc_start: 0.9507 (tp30) cc_final: 0.9302 (mm-30) REVERT: C 185 LYS cc_start: 0.9599 (mtpt) cc_final: 0.9377 (mtpp) REVERT: C 191 MET cc_start: 0.8426 (tpt) cc_final: 0.8015 (tpp) outliers start: 14 outliers final: 2 residues processed: 769 average time/residue: 0.5119 time to fit residues: 646.9092 Evaluate side-chains 546 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 544 time to evaluate : 4.768 ------------------------------------------------------------------------------- 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: 6.9990 chunk 341 optimal weight: 8.9990 chunk 235 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 455 optimal weight: 8.9990 chunk 482 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 431 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- 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 2 779 HIS ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 398 HIS 3 493 GLN ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 569 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 HIS ** 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** ** 6 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 57 GLN ** c 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 162 ASN D 183 HIS ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 40680 Z= 0.265 Angle : 0.868 14.794 54963 Z= 0.450 Chirality : 0.048 0.412 6368 Planarity : 0.005 0.193 7045 Dihedral : 6.079 43.426 5476 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.90 % Favored : 90.20 % Rotamer: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 3.71 % Twisted Proline : 0.53 % Twisted General : 0.21 % 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: -1.90 (0.11), residues: 4931 helix: -0.28 (0.11), residues: 1991 sheet: -1.76 (0.19), residues: 641 loop : -1.98 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 478 HIS 0.015 0.002 HIS 5 155 PHE 0.037 0.002 PHE 5 357 TYR 0.030 0.002 TYR C 4 ARG 0.012 0.001 ARG 5 549 *********************** 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 742 residues out of total 4511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 736 time to evaluate : 4.777 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 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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