Starting phenix.real_space_refine on Sun Mar 24 06:37:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc7_6536/03_2024/3jc7_6536_neut.pdb" } resolution = 4.8 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 177 5.16 5 C 25508 2.51 5 N 6978 2.21 5 O 7634 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 483": "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 ARG 607": "NH1" <-> "NH2" 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 407": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "5 PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 781": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 303": "NH1" <-> "NH2" Residue "7 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 400": "NH1" <-> "NH2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Residue "c ARG 68": "NH1" <-> "NH2" Residue "c ARG 69": "NH1" <-> "NH2" Residue "c ARG 117": "NH1" <-> "NH2" Residue "c PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 226": "NH1" <-> "NH2" Residue "c ARG 307": "NH1" <-> "NH2" Residue "c ARG 398": "NH1" <-> "NH2" Residue "c TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 406": "NH1" <-> "NH2" Residue "c ARG 411": "NH1" <-> "NH2" Residue "c ARG 472": "NH1" <-> "NH2" Residue "c PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 547": "NH1" <-> "NH2" Residue "c TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 587": "NH1" <-> "NH2" Residue "c TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 634": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40298 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 4531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4531 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 537} Chain breaks: 5 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: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4521 Classifications: {'peptide': 577} Link IDs: {'CIS': 18, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 6 Chain: "4" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4911 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 22, 'PTRANS': 23, 'TRANS': 575} Chain breaks: 5 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: 5172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5172 Classifications: {'peptide': 654} Link IDs: {'CIS': 16, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 612} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5204 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 32, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 613} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 116 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': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "7" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5176 Classifications: {'peptide': 657} Link IDs: {'CIS': 26, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 601} 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 Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25979 SG CYS 7 262 75.756 178.148 121.748 1.00167.77 S ATOM 26193 SG CYS 7 289 75.184 179.072 125.109 1.00194.98 S Time building chain proxies: 19.53, per 1000 atoms: 0.48 Number of scatterers: 40298 At special positions: 0 Unit cell: (172.71, 217.15, 149.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 177 16.00 O 7634 8.00 N 6978 7.00 C 25508 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: 15.24 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 71001 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 289 " 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9694 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 40 sheets defined 44.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 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: 3.999A 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: 3.913A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.522A 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: 4.345A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 502 removed outlier: 4.196A 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: 4.458A 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: 3.627A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 3.506A 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: 4.038A 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: 3.772A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 705 removed outlier: 3.561A 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: 4.468A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.047A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.811A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 858 removed outlier: 3.767A 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: 3.882A 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: 4.144A 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: 3.552A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 removed outlier: 3.537A 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: 3.811A 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: 3.925A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 461 through 465 Processing helix chain '3' and resid 479 through 491 removed outlier: 3.879A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 543 removed outlier: 3.585A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 569 removed outlier: 4.115A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 654 through 666 removed outlier: 3.914A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 675 through 694 removed outlier: 3.526A 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: 3.765A 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: 3.572A 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: 3.728A 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: 3.930A pdb=" N LEU 4 506 " --> pdb=" O THR 4 502 " (cutoff:3.500A) removed outlier: 3.526A 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: 4.615A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.554A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.869A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.030A 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: 3.799A 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: 3.559A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 762 through 779 removed outlier: 3.734A pdb=" N ALA 4 766 " --> pdb=" O ILE 4 762 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS 4 767 " --> pdb=" O THR 4 763 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) 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: 3.616A pdb=" N ALA 4 825 " --> pdb=" O ASP 4 821 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.827A 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: 4.165A 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: 4.191A 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 350 through 361 removed outlier: 3.761A pdb=" N GLU 5 354 " --> pdb=" O THR 5 350 " (cutoff:3.500A) 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: 3.869A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 removed outlier: 3.676A pdb=" N LEU 5 471 " --> pdb=" O GLY 5 467 " (cutoff:3.500A) Processing helix chain '5' and resid 487 through 500 removed outlier: 3.722A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.878A 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 564 through 574 Processing helix chain '5' and resid 579 through 592 Processing helix chain '5' and resid 596 through 610 removed outlier: 3.653A pdb=" N LYS 5 600 " --> pdb=" O ILE 5 596 " (cutoff:3.500A) removed outlier: 4.011A 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 667 removed outlier: 3.571A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 4.067A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER 5 693 " --> pdb=" O MET 5 689 " (cutoff:3.500A) Processing helix chain '5' and resid 707 through 712 Processing helix chain '5' and resid 714 through 719 Processing helix chain '5' and resid 728 through 737 Processing helix chain '5' and resid 744 through 759 Processing helix chain '6' and resid 106 through 121 removed outlier: 3.647A 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: 4.193A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.879A 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: 4.091A 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: 3.781A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.044A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.971A 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 720 through 736 Processing helix chain '6' and resid 749 through 759 removed outlier: 3.932A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 783 removed outlier: 3.656A pdb=" N LEU 6 773 " --> pdb=" O ALA 6 769 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 6 774 " --> pdb=" O ARG 6 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS 6 782 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 4.158A 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: 3.547A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 837 removed outlier: 3.559A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '6' and resid 906 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: 3.961A pdb=" N ILE 6 936 " --> pdb=" O THR 6 932 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.818A 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: 3.529A 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: 3.786A 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: 3.622A 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: 3.634A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 4.303A 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: 4.094A 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: 3.500A 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: 3.699A 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: 3.571A pdb=" N ASN 7 657 " --> pdb=" O SER 7 653 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.656A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 3.565A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.781A 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: 3.593A pdb=" N GLN c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 74 removed outlier: 4.204A 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: 3.520A pdb=" N PHE c 95 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.929A pdb=" N ILE c 134 " --> pdb=" O ASN c 130 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.945A 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: 3.709A 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: 4.529A 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: 3.701A pdb=" N LYS c 347 " --> pdb=" O TYR c 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 367 removed outlier: 3.753A pdb=" N LYS c 357 " --> pdb=" O GLU c 353 " (cutoff:3.500A) removed outlier: 4.320A 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: 3.628A 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: 3.671A 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: 3.975A 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: 3.651A 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: 3.589A pdb=" N ILE c 612 " --> pdb=" O ALA c 608 " (cutoff:3.500A) Processing helix chain 'c' and resid 633 through 646 removed outlier: 4.485A 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: 4.026A 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: 3.697A 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: 3.789A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.030A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.647A 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: 3.652A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.417A 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: 3.537A 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: 3.578A 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: 3.856A 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: 3.667A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 4.384A 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: 4.090A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.202A 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: 3.926A 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: 3.904A 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: 4.394A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.682A 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: 3.742A 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: 3.521A 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: 8.766A 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: 3.521A 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: 4.144A 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: 6.188A 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: 6.820A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 7.012A 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: 4.015A 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: 7.104A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.336A 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: 7.175A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.198A pdb=" N GLU 4 434 " --> pdb=" O LYS 4 467 " (cutoff:3.500A) removed outlier: 3.539A 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: 6.521A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 606 through 607 Processing sheet with id= R, first strand: chain '4' and resid 653 through 656 Processing sheet with id= S, first strand: chain '5' and resid 60 through 63 removed outlier: 6.245A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '5' and resid 298 through 301 removed outlier: 8.912A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.589A 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: 3.573A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 190 through 193 removed outlier: 6.898A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 436 through 440 removed outlier: 3.845A pdb=" N ASP 5 480 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 3.718A 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= W, first strand: chain '5' and resid 501 through 503 Processing sheet with id= X, first strand: chain '6' and resid 150 through 154 removed outlier: 3.675A 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= Y, first strand: chain '6' and resid 273 through 274 Processing sheet with id= Z, 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: 6.422A 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= AA, first strand: chain '6' and resid 404 through 405 Processing sheet with id= AB, 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: 6.223A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.930A 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= AC, first strand: chain '6' and resid 660 through 664 Processing sheet with id= AD, first strand: chain '7' and resid 77 through 81 Processing sheet with id= AE, 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= AF, 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= AG, 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= AH, first strand: chain '7' and resid 481 through 484 removed outlier: 6.604A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (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: 6.457A 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: 6.271A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) Processing sheet with id= AI, 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: 8.206A pdb=" N LEU c 123 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 6.744A 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: 3.627A pdb=" N ILE c 58 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 188 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'c' and resid 318 through 321 removed outlier: 5.507A pdb=" N THR c 412 " --> pdb=" O ILE c 419 " (cutoff:3.500A) removed outlier: 7.060A 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= AK, 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= AL, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.020A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 69 through 72 Processing sheet with id= AN, 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) 1494 hydrogen bonds defined for protein. 4290 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: 15.67 Time building geometry restraints manager: 16.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 6807 1.28 - 1.42: 9796 1.42 - 1.56: 23992 1.56 - 1.70: 57 1.70 - 1.84: 290 Bond restraints: 40942 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 GLU 6 929 " pdb=" O GLU 6 929 " ideal model delta sigma weight residual 1.235 1.377 -0.141 1.26e-02 6.30e+03 1.26e+02 bond pdb=" C GLU 6 930 " pdb=" N LEU 6 931 " ideal model delta sigma weight residual 1.332 1.441 -0.108 1.40e-02 5.10e+03 5.97e+01 bond pdb=" C PHE 5 714 " pdb=" O PHE 5 714 " ideal model delta sigma weight residual 1.235 1.138 0.097 1.26e-02 6.30e+03 5.92e+01 bond pdb=" C GLU 6 929 " pdb=" N GLU 6 930 " ideal model delta sigma weight residual 1.332 1.238 0.094 1.40e-02 5.10e+03 4.55e+01 ... (remaining 40937 not shown) Histogram of bond angle deviations from ideal: 92.70 - 102.37: 147 102.37 - 112.04: 19762 112.04 - 121.70: 25909 121.70 - 131.37: 9412 131.37 - 141.04: 91 Bond angle restraints: 55321 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=" OG1 THR 5 732 " pdb=" CB THR 5 732 " pdb=" CG2 THR 5 732 " ideal model delta sigma weight residual 109.30 141.04 -31.74 2.00e+00 2.50e-01 2.52e+02 angle pdb=" C GLU 4 378 " pdb=" N PRO 4 379 " pdb=" CA PRO 4 379 " ideal model delta sigma weight residual 119.56 134.49 -14.93 1.02e+00 9.61e-01 2.14e+02 angle pdb=" C CYS 6 333 " pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " ideal model delta sigma weight residual 119.84 136.22 -16.38 1.25e+00 6.40e-01 1.72e+02 angle pdb=" CA ARG 5 742 " pdb=" CB ARG 5 742 " pdb=" CG ARG 5 742 " ideal model delta sigma weight residual 114.10 137.38 -23.28 2.00e+00 2.50e-01 1.36e+02 ... (remaining 55316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 24502 26.95 - 53.91: 598 53.91 - 80.86: 62 80.86 - 107.82: 14 107.82 - 134.77: 2 Dihedral angle restraints: 25178 sinusoidal: 10286 harmonic: 14892 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 -45.23 -134.77 0 5.00e+00 4.00e-02 7.27e+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 45.76 134.24 0 5.00e+00 4.00e-02 7.21e+02 dihedral pdb=" N THR 5 728 " pdb=" C THR 5 728 " pdb=" CA THR 5 728 " pdb=" CB THR 5 728 " ideal model delta harmonic sigma weight residual 123.40 156.89 -33.49 0 2.50e+00 1.60e-01 1.79e+02 ... (remaining 25175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.301: 6400 0.301 - 0.603: 11 0.603 - 0.904: 1 0.904 - 1.205: 2 1.205 - 1.506: 1 Chirality restraints: 6415 Sorted by residual: chirality pdb=" CA THR 5 728 " pdb=" N THR 5 728 " pdb=" C THR 5 728 " pdb=" CB THR 5 728 " both_signs ideal model delta sigma weight residual False 2.53 1.02 1.51 2.00e-01 2.50e+01 5.67e+01 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 2.59e+01 chirality pdb=" CB THR 5 732 " pdb=" CA THR 5 732 " pdb=" OG1 THR 5 732 " pdb=" CG2 THR 5 732 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 6412 not shown) Planarity restraints: 7087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR 5 728 " 0.051 2.00e-02 2.50e+03 1.07e-01 1.13e+02 pdb=" C THR 5 728 " -0.184 2.00e-02 2.50e+03 pdb=" O THR 5 728 " 0.068 2.00e-02 2.50e+03 pdb=" N SER 5 729 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 906 " -0.104 2.00e-02 2.50e+03 5.78e-02 6.67e+01 pdb=" CG TYR 6 906 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 906 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 906 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 906 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 906 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR 6 906 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR 6 906 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 954 " 0.055 2.00e-02 2.50e+03 5.53e-02 6.13e+01 pdb=" CG TYR 6 954 " 0.011 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 ... (remaining 7084 not shown) Histogram of nonbonded interaction distances: 0.16 - 1.11: 9 1.11 - 2.06: 143 2.06 - 3.01: 25165 3.01 - 3.95: 105263 3.95 - 4.90: 186759 Warning: very small nonbonded interaction distances. Nonbonded interactions: 317339 Sorted by model distance: nonbonded pdb=" NE ARG 3 570 " pdb=" CZ ARG 5 613 " model vdw 0.163 3.350 nonbonded pdb=" C GLY 2 801 " pdb=" NH2 ARG 5 529 " model vdw 0.474 3.350 nonbonded pdb=" OE1 GLU 4 532 " pdb=" ND2 ASN 4 716 " model vdw 0.491 2.520 nonbonded pdb=" CD PRO 3 288 " pdb=" O GLY 5 508 " model vdw 0.620 3.440 nonbonded pdb=" NZ LYS 3 188 " pdb=" CB ARG 5 455 " model vdw 0.722 3.520 ... (remaining 317334 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.950 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 105.390 Find NCS groups from input model: 2.250 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5383 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 40942 Z= 0.613 Angle : 1.575 31.737 55321 Z= 1.022 Chirality : 0.067 1.506 6415 Planarity : 0.007 0.107 7087 Dihedral : 12.163 134.771 15478 Min Nonbonded Distance : 0.163 Molprobity Statistics. All-atom Clashscore : 42.92 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.53 % Favored : 90.14 % Rotamer: Outliers : 0.45 % Allowed : 4.82 % Favored : 94.74 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.48 % Twisted Proline : 0.53 % Twisted General : 0.54 % 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: -4.10 (0.09), residues: 4969 helix: -3.23 (0.08), residues: 1951 sheet: -2.14 (0.17), residues: 599 loop : -2.34 (0.11), residues: 2419 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 0.066 0.003 PHE 5 714 TYR 0.113 0.003 TYR 6 954 ARG 0.035 0.001 ARG 6 958 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1043 time to evaluate : 4.730 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: 2 215 LEU cc_start: 0.9052 (tp) cc_final: 0.8705 (tp) REVERT: 2 267 MET cc_start: 0.8214 (ttp) cc_final: 0.7965 (mtt) REVERT: 2 279 THR cc_start: 0.8251 (m) cc_final: 0.7961 (p) REVERT: 2 323 VAL cc_start: 0.7981 (t) cc_final: 0.7633 (t) REVERT: 2 456 ILE cc_start: 0.9121 (mm) cc_final: 0.8890 (mt) REVERT: 3 100 LEU cc_start: 0.8323 (mt) cc_final: 0.8090 (mm) REVERT: 3 164 HIS cc_start: 0.7128 (m170) cc_final: 0.6583 (m170) REVERT: 3 176 LEU cc_start: 0.8028 (tt) cc_final: 0.7203 (tt) REVERT: 3 185 ILE cc_start: 0.7967 (mm) cc_final: 0.7621 (mm) REVERT: 3 213 ASP cc_start: 0.6516 (t0) cc_final: 0.5962 (p0) REVERT: 3 301 LEU cc_start: 0.8682 (pp) cc_final: 0.8385 (pp) REVERT: 3 406 LEU cc_start: 0.7248 (tt) cc_final: 0.7005 (tt) REVERT: 3 413 THR cc_start: 0.6693 (m) cc_final: 0.6314 (m) REVERT: 3 486 ILE cc_start: 0.8654 (mt) cc_final: 0.8378 (mt) REVERT: 3 536 PRO cc_start: 0.4780 (Cg_endo) cc_final: 0.4449 (Cg_exo) REVERT: 3 662 TYR cc_start: 0.6126 (t80) cc_final: 0.5303 (t80) REVERT: 4 233 MET cc_start: 0.4542 (ttt) cc_final: 0.4060 (tmm) REVERT: 5 41 ASP cc_start: 0.8672 (m-30) cc_final: 0.8445 (t0) REVERT: 5 169 THR cc_start: 0.7902 (p) cc_final: 0.7396 (t) REVERT: 5 355 GLU cc_start: 0.9198 (tt0) cc_final: 0.8781 (tt0) REVERT: 5 383 ASP cc_start: 0.8231 (m-30) cc_final: 0.7626 (p0) REVERT: 5 384 ILE cc_start: 0.8113 (mt) cc_final: 0.7486 (mm) REVERT: 5 426 LEU cc_start: 0.7991 (mt) cc_final: 0.7429 (mp) REVERT: 5 429 VAL cc_start: 0.9423 (t) cc_final: 0.9003 (p) REVERT: 5 478 CYS cc_start: 0.6562 (m) cc_final: 0.5624 (m) REVERT: 5 603 ILE cc_start: 0.8868 (mt) cc_final: 0.8635 (mm) REVERT: 5 605 TYR cc_start: 0.8031 (t80) cc_final: 0.7433 (t80) REVERT: 6 276 ILE cc_start: 0.7376 (pp) cc_final: 0.6951 (pt) REVERT: 6 378 ASP cc_start: 0.8702 (t0) cc_final: 0.7930 (p0) REVERT: 6 457 CYS cc_start: 0.7217 (p) cc_final: 0.6376 (m) REVERT: 6 824 ILE cc_start: 0.0181 (mm) cc_final: -0.0197 (mt) REVERT: 7 64 MET cc_start: 0.8246 (mtt) cc_final: 0.7964 (mmm) REVERT: 7 235 LEU cc_start: 0.8386 (mt) cc_final: 0.7845 (mp) REVERT: 7 355 PHE cc_start: 0.6936 (t80) cc_final: 0.6294 (t80) REVERT: 7 428 VAL cc_start: 0.8594 (t) cc_final: 0.8374 (t) REVERT: 7 540 VAL cc_start: 0.8248 (t) cc_final: 0.7737 (t) REVERT: c 324 TYR cc_start: 0.7852 (m-80) cc_final: 0.6881 (m-10) REVERT: c 335 TYR cc_start: 0.8217 (t80) cc_final: 0.7986 (t80) REVERT: c 359 LEU cc_start: 0.9457 (tp) cc_final: 0.9190 (tt) REVERT: c 366 MET cc_start: 0.8586 (mtt) cc_final: 0.8280 (mtt) REVERT: c 368 ILE cc_start: 0.9090 (mt) cc_final: 0.8885 (mt) REVERT: c 376 THR cc_start: 0.9028 (m) cc_final: 0.8720 (p) REVERT: c 379 TYR cc_start: 0.7384 (m-10) cc_final: 0.5923 (m-80) REVERT: c 431 LEU cc_start: 0.9274 (mt) cc_final: 0.8981 (mt) REVERT: c 485 ASP cc_start: 0.8947 (m-30) cc_final: 0.8650 (p0) REVERT: c 605 PHE cc_start: 0.8808 (m-80) cc_final: 0.8136 (m-10) REVERT: D 65 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8901 (tptt) REVERT: D 102 SER cc_start: 0.9445 (t) cc_final: 0.9185 (p) REVERT: D 135 ARG cc_start: 0.6534 (ttp-110) cc_final: 0.6043 (ttm170) REVERT: B 73 LEU cc_start: 0.9046 (tp) cc_final: 0.8492 (tt) REVERT: A 1 MET cc_start: 0.4065 (ptp) cc_final: 0.3647 (ptp) REVERT: A 39 ASN cc_start: 0.9359 (m110) cc_final: 0.9115 (m110) REVERT: A 133 GLU cc_start: 0.9334 (tt0) cc_final: 0.9027 (tm-30) REVERT: A 181 PHE cc_start: 0.6632 (m-10) cc_final: 0.5816 (m-80) REVERT: A 183 LEU cc_start: 0.8631 (mm) cc_final: 0.8304 (mm) REVERT: C 137 HIS cc_start: 0.8508 (m170) cc_final: 0.8294 (m170) outliers start: 20 outliers final: 3 residues processed: 1062 average time/residue: 0.5854 time to fit residues: 958.5404 Evaluate side-chains 553 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 550 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 423 optimal weight: 7.9990 chunk 380 optimal weight: 0.9990 chunk 211 optimal weight: 50.0000 chunk 129 optimal weight: 3.9990 chunk 256 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 455 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN ** 2 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 658 ASN 2 809 HIS 2 849 GLN 2 856 GLN 3 29 GLN 3 239 ASN ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 417 GLN 3 503 HIS 3 554 ASN 3 661 GLN 3 673 GLN ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN 4 413 HIS 4 576 GLN ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 579 ASN 5 758 HIS ** 6 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN 6 698 ASN 6 799 GLN 7 87 GLN 7 89 GLN ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 243 GLN c 249 ASN ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 395 ASN c 500 GLN c 604 ASN D 160 GLN B 9 GLN B 146 GLN A 28 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN A 202 GLN C 21 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40942 Z= 0.295 Angle : 0.977 17.562 55321 Z= 0.509 Chirality : 0.052 0.512 6415 Planarity : 0.006 0.114 7087 Dihedral : 6.708 68.449 5514 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 1.05 % Allowed : 8.07 % Favored : 90.88 % Rotamer: Outliers : 0.31 % Allowed : 3.99 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.72 % Twisted Proline : 1.06 % 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: -2.62 (0.11), residues: 4969 helix: -1.38 (0.10), residues: 2004 sheet: -1.80 (0.18), residues: 588 loop : -1.97 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP 6 939 HIS 0.023 0.002 HIS 5 494 PHE 0.053 0.003 PHE 6 641 TYR 0.025 0.002 TYR 4 457 ARG 0.038 0.001 ARG 3 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 739 time to evaluate : 4.824 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: 2 215 LEU cc_start: 0.9069 (tp) cc_final: 0.8733 (tp) REVERT: 2 259 PHE cc_start: 0.9143 (m-10) cc_final: 0.8787 (m-80) REVERT: 2 267 MET cc_start: 0.8359 (ttp) cc_final: 0.8130 (ptm) REVERT: 2 382 TYR cc_start: 0.8362 (m-80) cc_final: 0.8122 (m-80) REVERT: 2 413 ASP cc_start: 0.8798 (m-30) cc_final: 0.8580 (m-30) REVERT: 2 450 ILE cc_start: 0.8514 (mp) cc_final: 0.8219 (mm) REVERT: 2 451 ILE cc_start: 0.7731 (mp) cc_final: 0.6881 (tp) REVERT: 2 501 MET cc_start: 0.7417 (mmm) cc_final: 0.7149 (mmm) REVERT: 3 176 LEU cc_start: 0.7775 (tt) cc_final: 0.7059 (tt) REVERT: 3 213 ASP cc_start: 0.6765 (t0) cc_final: 0.6123 (p0) REVERT: 3 298 PHE cc_start: 0.7494 (t80) cc_final: 0.7173 (t80) REVERT: 3 473 ASP cc_start: 0.6548 (t0) cc_final: 0.6298 (t70) REVERT: 3 490 MET cc_start: 0.4772 (ptp) cc_final: 0.4440 (ptm) REVERT: 3 662 TYR cc_start: 0.6182 (t80) cc_final: 0.5951 (t80) REVERT: 4 280 MET cc_start: 0.7557 (mpp) cc_final: 0.7154 (mtt) REVERT: 4 331 LEU cc_start: 0.9217 (pp) cc_final: 0.8762 (pp) REVERT: 4 423 LEU cc_start: 0.9146 (mt) cc_final: 0.8865 (mp) REVERT: 4 702 PHE cc_start: 0.6223 (m-80) cc_final: 0.5924 (m-80) REVERT: 5 41 ASP cc_start: 0.8705 (m-30) cc_final: 0.8337 (t0) REVERT: 5 45 ILE cc_start: 0.8062 (mm) cc_final: 0.7586 (mm) REVERT: 5 48 ASP cc_start: 0.9377 (p0) cc_final: 0.8499 (t0) REVERT: 5 134 THR cc_start: 0.8743 (m) cc_final: 0.8506 (t) REVERT: 5 151 LEU cc_start: 0.9338 (mt) cc_final: 0.9046 (pp) REVERT: 5 284 ASN cc_start: 0.8670 (t0) cc_final: 0.8097 (t0) REVERT: 5 355 GLU cc_start: 0.9329 (tt0) cc_final: 0.9075 (tp30) REVERT: 5 359 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8050 (tm-30) REVERT: 5 383 ASP cc_start: 0.8256 (m-30) cc_final: 0.7636 (p0) REVERT: 5 384 ILE cc_start: 0.8392 (mt) cc_final: 0.7836 (pt) REVERT: 5 429 VAL cc_start: 0.9353 (t) cc_final: 0.8938 (p) REVERT: 5 497 MET cc_start: 0.5846 (ptm) cc_final: 0.5269 (ppp) REVERT: 5 605 TYR cc_start: 0.7761 (t80) cc_final: 0.7426 (t80) REVERT: 6 143 MET cc_start: 0.8944 (mmp) cc_final: 0.8068 (tmm) REVERT: 6 378 ASP cc_start: 0.7913 (t0) cc_final: 0.7553 (p0) REVERT: 6 400 VAL cc_start: 0.8455 (m) cc_final: 0.8094 (p) REVERT: 6 457 CYS cc_start: 0.6848 (p) cc_final: 0.5802 (m) REVERT: 7 18 PHE cc_start: 0.8653 (t80) cc_final: 0.8413 (t80) REVERT: 7 142 ILE cc_start: 0.9063 (mt) cc_final: 0.8839 (mt) REVERT: 7 235 LEU cc_start: 0.8818 (mt) cc_final: 0.8210 (mp) REVERT: 7 355 PHE cc_start: 0.7081 (t80) cc_final: 0.6524 (t80) REVERT: 7 376 LEU cc_start: 0.7916 (tp) cc_final: 0.7437 (tp) REVERT: 7 428 VAL cc_start: 0.8579 (t) cc_final: 0.8162 (t) REVERT: 7 621 MET cc_start: 0.7411 (ttp) cc_final: 0.7025 (ttt) REVERT: c 271 TRP cc_start: 0.7200 (t-100) cc_final: 0.6977 (t60) REVERT: c 324 TYR cc_start: 0.7679 (m-80) cc_final: 0.7313 (m-10) REVERT: c 359 LEU cc_start: 0.9504 (tp) cc_final: 0.8571 (tp) REVERT: c 362 MET cc_start: 0.9495 (tmm) cc_final: 0.9017 (tmm) REVERT: c 363 PHE cc_start: 0.8578 (m-80) cc_final: 0.7833 (m-80) REVERT: c 378 LEU cc_start: 0.8573 (mt) cc_final: 0.8353 (mt) REVERT: c 379 TYR cc_start: 0.7591 (m-10) cc_final: 0.5979 (m-80) REVERT: c 380 MET cc_start: 0.8366 (ttp) cc_final: 0.7605 (tmm) REVERT: c 388 LEU cc_start: 0.8925 (mt) cc_final: 0.8488 (mt) REVERT: c 392 PHE cc_start: 0.8249 (m-10) cc_final: 0.7883 (m-10) REVERT: c 485 ASP cc_start: 0.9005 (m-30) cc_final: 0.8715 (p0) REVERT: c 607 MET cc_start: 0.7387 (mpp) cc_final: 0.7120 (mpp) REVERT: D 102 SER cc_start: 0.9575 (t) cc_final: 0.9291 (p) REVERT: D 233 ASN cc_start: 0.7313 (p0) cc_final: 0.7096 (p0) REVERT: B 56 ASP cc_start: 0.8358 (p0) cc_final: 0.7847 (m-30) REVERT: B 73 LEU cc_start: 0.8937 (tp) cc_final: 0.8052 (tp) REVERT: B 190 ASP cc_start: 0.8231 (m-30) cc_final: 0.7643 (m-30) REVERT: A 36 ILE cc_start: 0.6954 (pt) cc_final: 0.6313 (pt) REVERT: A 39 ASN cc_start: 0.9358 (m110) cc_final: 0.9096 (m110) REVERT: A 46 ASN cc_start: 0.9091 (m110) cc_final: 0.8864 (m110) REVERT: A 110 MET cc_start: -0.1024 (tpt) cc_final: -0.2415 (tpt) REVERT: C 79 MET cc_start: 0.8548 (pmm) cc_final: 0.8002 (pmm) REVERT: C 173 GLU cc_start: 0.9211 (mp0) cc_final: 0.8241 (pt0) outliers start: 14 outliers final: 2 residues processed: 752 average time/residue: 0.5846 time to fit residues: 708.5208 Evaluate side-chains 513 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 511 time to evaluate : 4.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 379 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 456 optimal weight: 7.9990 chunk 493 optimal weight: 6.9990 chunk 406 optimal weight: 6.9990 chunk 452 optimal weight: 0.0040 chunk 155 optimal weight: 0.2980 chunk 366 optimal weight: 6.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 561 HIS ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 175 HIS 3 269 GLN ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 ASN ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 253 GLN ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 182 GLN 6 362 GLN 6 583 GLN ** 6 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 229 GLN 7 585 ASN 7 622 HIS ** 7 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 249 ASN ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 395 ASN c 575 ASN c 604 ASN D 110 ASN A 90 GLN A 188 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40942 Z= 0.229 Angle : 0.884 17.040 55321 Z= 0.459 Chirality : 0.049 0.392 6415 Planarity : 0.005 0.083 7087 Dihedral : 6.242 54.415 5514 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.39 % Favored : 90.72 % Rotamer: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 3.75 % 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: -2.00 (0.11), residues: 4969 helix: -0.59 (0.11), residues: 2002 sheet: -1.61 (0.20), residues: 579 loop : -1.87 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 224 HIS 0.018 0.001 HIS 5 494 PHE 0.050 0.002 PHE 5 197 TYR 0.021 0.002 TYR 7 411 ARG 0.015 0.001 ARG 5 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 655 time to evaluate : 4.837 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: 2 215 LEU cc_start: 0.9074 (tp) cc_final: 0.8776 (tp) REVERT: 2 259 PHE cc_start: 0.9093 (m-10) cc_final: 0.8716 (m-80) REVERT: 2 267 MET cc_start: 0.8272 (ttp) cc_final: 0.8023 (ptm) REVERT: 2 414 LEU cc_start: 0.9209 (mp) cc_final: 0.8927 (mm) REVERT: 2 451 ILE cc_start: 0.7525 (mp) cc_final: 0.7017 (mm) REVERT: 2 501 MET cc_start: 0.7489 (mmm) cc_final: 0.7193 (mmm) REVERT: 3 176 LEU cc_start: 0.7737 (tt) cc_final: 0.7093 (tt) REVERT: 3 213 ASP cc_start: 0.6458 (t0) cc_final: 0.6084 (p0) REVERT: 3 261 MET cc_start: 0.8889 (mpp) cc_final: 0.8631 (mpp) REVERT: 4 322 ILE cc_start: 0.4367 (pt) cc_final: 0.3200 (pt) REVERT: 4 384 LEU cc_start: 0.9315 (tt) cc_final: 0.8983 (pp) REVERT: 4 400 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8299 (tp-100) REVERT: 4 423 LEU cc_start: 0.9159 (mt) cc_final: 0.8837 (mp) REVERT: 4 439 PHE cc_start: 0.8835 (t80) cc_final: 0.8568 (t80) REVERT: 4 649 MET cc_start: 0.0526 (mtt) cc_final: 0.0138 (mtt) REVERT: 4 702 PHE cc_start: 0.5958 (m-80) cc_final: 0.5655 (m-80) REVERT: 5 41 ASP cc_start: 0.8723 (m-30) cc_final: 0.8334 (t0) REVERT: 5 45 ILE cc_start: 0.7882 (mm) cc_final: 0.7533 (mm) REVERT: 5 48 ASP cc_start: 0.9271 (p0) cc_final: 0.8961 (t0) REVERT: 5 182 MET cc_start: 0.8929 (ppp) cc_final: 0.8719 (ppp) REVERT: 5 252 ASP cc_start: 0.8182 (t0) cc_final: 0.7768 (t0) REVERT: 5 257 LYS cc_start: 0.8980 (pttp) cc_final: 0.8733 (pttp) REVERT: 5 276 MET cc_start: 0.7237 (mpp) cc_final: 0.6284 (mpp) REVERT: 5 283 THR cc_start: 0.9310 (p) cc_final: 0.8679 (p) REVERT: 5 359 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8121 (tm-30) REVERT: 5 383 ASP cc_start: 0.8270 (m-30) cc_final: 0.7655 (p0) REVERT: 5 384 ILE cc_start: 0.8109 (mt) cc_final: 0.7630 (pt) REVERT: 5 404 MET cc_start: 0.4159 (ppp) cc_final: 0.3880 (ppp) REVERT: 5 429 VAL cc_start: 0.9316 (t) cc_final: 0.9062 (p) REVERT: 5 469 MET cc_start: 0.7473 (pmm) cc_final: 0.7261 (pmm) REVERT: 5 497 MET cc_start: 0.5763 (ptm) cc_final: 0.5521 (ppp) REVERT: 6 143 MET cc_start: 0.8989 (mmp) cc_final: 0.8718 (mmm) REVERT: 6 378 ASP cc_start: 0.7984 (t0) cc_final: 0.7692 (p0) REVERT: 6 400 VAL cc_start: 0.8463 (m) cc_final: 0.7991 (p) REVERT: 6 457 CYS cc_start: 0.6919 (p) cc_final: 0.5796 (m) REVERT: 6 824 ILE cc_start: 0.0645 (mm) cc_final: 0.0331 (mt) REVERT: 7 18 PHE cc_start: 0.8638 (t80) cc_final: 0.8401 (t80) REVERT: 7 142 ILE cc_start: 0.9183 (mt) cc_final: 0.8894 (mt) REVERT: 7 235 LEU cc_start: 0.8761 (mt) cc_final: 0.8138 (mp) REVERT: 7 355 PHE cc_start: 0.7274 (t80) cc_final: 0.6475 (t80) REVERT: 7 376 LEU cc_start: 0.8076 (tp) cc_final: 0.7571 (tp) REVERT: 7 428 VAL cc_start: 0.8633 (t) cc_final: 0.8276 (t) REVERT: 7 621 MET cc_start: 0.7621 (ttp) cc_final: 0.6950 (ttt) REVERT: c 44 MET cc_start: 0.8749 (mmm) cc_final: 0.8112 (mmm) REVERT: c 271 TRP cc_start: 0.7296 (t-100) cc_final: 0.7013 (t60) REVERT: c 336 ASP cc_start: 0.9291 (m-30) cc_final: 0.9040 (p0) REVERT: c 359 LEU cc_start: 0.9545 (tp) cc_final: 0.9206 (tp) REVERT: c 362 MET cc_start: 0.9502 (tmm) cc_final: 0.9121 (tmm) REVERT: c 380 MET cc_start: 0.8577 (ttp) cc_final: 0.7427 (tmm) REVERT: c 485 ASP cc_start: 0.9049 (m-30) cc_final: 0.8731 (p0) REVERT: c 567 MET cc_start: 0.7552 (mmp) cc_final: 0.7282 (mtm) REVERT: c 605 PHE cc_start: 0.8885 (m-80) cc_final: 0.8487 (m-10) REVERT: c 607 MET cc_start: 0.7329 (mpp) cc_final: 0.7116 (mpp) REVERT: D 102 SER cc_start: 0.9556 (t) cc_final: 0.9303 (p) REVERT: D 183 HIS cc_start: 0.8483 (t70) cc_final: 0.8187 (t70) REVERT: D 216 VAL cc_start: 0.6142 (OUTLIER) cc_final: 0.5770 (m) REVERT: D 220 ASP cc_start: 0.7773 (t0) cc_final: 0.7497 (t0) REVERT: D 277 MET cc_start: 0.5813 (mmm) cc_final: 0.5375 (tpp) REVERT: B 56 ASP cc_start: 0.8383 (p0) cc_final: 0.7834 (m-30) REVERT: B 91 GLN cc_start: 0.6210 (mp10) cc_final: 0.5922 (mm-40) REVERT: A 17 LYS cc_start: 0.8624 (tptp) cc_final: 0.8418 (tptp) REVERT: A 36 ILE cc_start: 0.6826 (pt) cc_final: 0.6283 (pt) REVERT: A 39 ASN cc_start: 0.9357 (m110) cc_final: 0.9153 (m110) REVERT: A 42 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8764 (mmmt) REVERT: A 110 MET cc_start: -0.1242 (tpt) cc_final: -0.2509 (tpt) REVERT: A 112 SER cc_start: 0.6880 (t) cc_final: 0.6257 (t) REVERT: C 79 MET cc_start: 0.8722 (pmm) cc_final: 0.8221 (pmm) REVERT: C 173 GLU cc_start: 0.9076 (mp0) cc_final: 0.8433 (pt0) outliers start: 8 outliers final: 3 residues processed: 663 average time/residue: 0.5425 time to fit residues: 575.5054 Evaluate side-chains 500 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 496 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 451 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 458 optimal weight: 20.0000 chunk 485 optimal weight: 30.0000 chunk 239 optimal weight: 0.0370 chunk 434 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 overall best weight: 6.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 454 ASN 2 561 HIS ** 3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 569 HIS ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 413 HIS 4 757 HIS ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 185 ASN ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 347 ASN 6 659 GLN ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 384 HIS ** 7 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 286 GLN ** c 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 604 ASN D 183 HIS B 81 GLN B 128 ASN A 90 GLN A 202 GLN C 103 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 40942 Z= 0.288 Angle : 0.885 16.801 55321 Z= 0.458 Chirality : 0.048 0.397 6415 Planarity : 0.005 0.063 7087 Dihedral : 6.057 40.139 5514 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.85 % Favored : 90.28 % Rotamer: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 3.72 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 4969 helix: -0.27 (0.11), residues: 2018 sheet: -1.57 (0.20), residues: 564 loop : -1.87 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 3 111 HIS 0.015 0.002 HIS 5 494 PHE 0.038 0.002 PHE 6 641 TYR 0.025 0.002 TYR 2 434 ARG 0.013 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9938 Ramachandran restraints generated. 4969 Oldfield, 0 Emsley, 4969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 603 time to evaluate : 4.506 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 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