Starting phenix.real_space_refine on Sat Mar 16 22:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gmk_9525/03_2024/5gmk_9525_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 407 5.49 5 Mg 6 5.21 5 S 242 5.16 5 C 46149 2.51 5 N 13144 2.21 5 O 15318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1490": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 252": "NH1" <-> "NH2" Residue "Q GLU 257": "OE1" <-> "OE2" Residue "Q ARG 261": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 42": "NH1" <-> "NH2" Residue "Z ARG 53": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z ARG 108": "NH1" <-> "NH2" Residue "Z GLU 144": "OE1" <-> "OE2" Residue "Z ARG 149": "NH1" <-> "NH2" Residue "Z GLU 175": "OE1" <-> "OE2" Residue "Z ARG 178": "NH1" <-> "NH2" Residue "Z ARG 191": "NH1" <-> "NH2" Residue "Z ARG 201": "NH1" <-> "NH2" Residue "Z GLU 246": "OE1" <-> "OE2" Residue "Z ARG 382": "NH1" <-> "NH2" Residue "Z ARG 439": "NH1" <-> "NH2" Residue "c ARG 85": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "v GLU 609": "OE1" <-> "OE2" Residue "n GLU 55": "OE1" <-> "OE2" Residue "n ARG 60": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "o GLU 24": "OE1" <-> "OE2" Residue "o GLU 29": "OE1" <-> "OE2" Residue "o GLU 48": "OE1" <-> "OE2" Residue "o GLU 129": "OE1" <-> "OE2" Residue "o GLU 132": "OE1" <-> "OE2" Residue "p GLU 24": "OE1" <-> "OE2" Residue "p GLU 29": "OE1" <-> "OE2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "p GLU 94": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p GLU 132": "OE1" <-> "OE2" Residue "q GLU 24": "OE1" <-> "OE2" Residue "q GLU 29": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "r GLU 24": "OE1" <-> "OE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r GLU 48": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 129": "OE1" <-> "OE2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "j ARG 30": "NH1" <-> "NH2" Residue "m ARG 88": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ARG 97": "NH1" <-> "NH2" Residue "s ARG 11": "NH1" <-> "NH2" Residue "s GLU 90": "OE1" <-> "OE2" Residue "w ARG 82": "NH1" <-> "NH2" Residue "x ARG 30": "NH1" <-> "NH2" Residue "z ARG 88": "NH1" <-> "NH2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e GLU 70": "OE1" <-> "OE2" Residue "e ARG 97": "NH1" <-> "NH2" 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: 75273 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 15775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1910, 15775 Classifications: {'peptide': 1910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 99, 'TRANS': 1809} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7019 Classifications: {'peptide': 878} Link IDs: {'PTRANS': 49, 'TRANS': 828} Chain breaks: 2 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2465 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 39, 'rna3p_pyr': 56} Link IDs: {'rna2p': 22, 'rna3p': 94} Chain breaks: 2 Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 21, 'rna3p': 81} Chain: "L" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2673 Classifications: {'RNA': 127} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 15, 'rna3p_pur': 48, 'rna3p_pyr': 58} Link IDs: {'rna2p': 21, 'rna3p': 105} Chain breaks: 6 Chain: "M" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 608 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 24} Chain: "B" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 6} Chain: "N" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2646 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 323} Chain: "P" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1583 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1472 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 3 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2089 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "S" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 560 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "Z" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3651 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 439} Chain breaks: 1 Chain: "c" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 2971 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 5, 'UNK:plan-1': 118, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 288 Chain: "d" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 3590 Classifications: {'peptide': 549} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 299} Link IDs: {'PTRANS': 5, 'TRANS': 543} Chain breaks: 21 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 309} Unresolved non-hydrogen planarities: 309 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 342 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "H" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 810 Classifications: {'peptide': 95} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 92} Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "v" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 3580 Classifications: {'peptide': 673} Incomplete info: {'backbone_only': 19, 'truncation_to_alanine': 535} Link IDs: {'PTRANS': 6, 'TRANS': 666} Chain breaks: 38 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1329 Unresolved non-hydrogen angles: 1967 Unresolved non-hydrogen dihedrals: 725 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 2, 'TYR:plan': 2, 'UNK:plan-1': 540, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 675 Chain: "n" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1890 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 280} Chain breaks: 9 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 472 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 338 Chain: "o" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "p" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "q" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2345 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 1052 Unresolved non-hydrogen dihedrals: 624 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 22, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 420 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "t" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 258 Chain: "k" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "i" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 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: "j" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "m" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "g" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "s" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "u" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "w" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 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: "x" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "z" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "e" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 528 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 513 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "b" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 841 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 167 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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 35823 SG CYS Q 13 69.815 144.140 124.941 1.00 0.00 S ATOM 36281 SG CYS Q 71 73.089 143.621 126.646 1.00 0.00 S ATOM 36296 SG CYS Q 73 71.485 146.721 127.323 1.00 0.00 S ATOM 36302 SG CYS Q 74 69.631 143.633 128.467 1.00 0.00 S ATOM 35981 SG CYS Q 34 83.818 147.023 133.999 1.00 0.00 S ATOM 36004 SG CYS Q 37 87.226 146.867 135.407 1.00 0.00 S ATOM 36203 SG CYS Q 61 86.441 147.413 131.701 1.00 0.00 S ATOM 36227 SG CYS Q 64 86.063 144.014 133.465 1.00 0.00 S ATOM 37792 SG CYS R 73 59.002 159.945 145.543 1.00 0.00 S ATOM 37854 SG CYS R 81 57.608 163.270 146.449 1.00 0.00 S ATOM 37894 SG CYS R 87 57.410 162.088 142.893 1.00 0.00 S ATOM 40747 SG CYS T 104 59.896 180.190 126.868 1.00 0.00 S ATOM 40753 SG CYS T 105 63.123 182.250 127.516 1.00 0.00 S ATOM 40778 SG CYS T 108 63.233 178.977 125.292 1.00 0.00 S ATOM 41092 SG CYS T 148 63.042 179.021 128.630 1.00 0.00 S ATOM 40747 SG CYS T 104 59.896 180.190 126.868 1.00 0.00 S ATOM 40881 SG CYS T 122 60.361 176.888 124.978 1.00 0.00 S ATOM 41102 SG CYS T 150 56.923 177.988 126.082 1.00 0.00 S ATOM 41123 SG CYS T 153 58.694 179.952 123.587 1.00 0.00 S ATOM 40778 SG CYS T 108 63.233 178.977 125.292 1.00 0.00 S ATOM 40867 SG CYS T 120 64.071 175.549 124.133 1.00 0.00 S ATOM 40881 SG CYS T 122 60.361 176.888 124.978 1.00 0.00 S ATOM 41069 SG CYS T 145 62.857 175.772 127.531 1.00 0.00 S ATOM 51772 SG CYS F 51 115.943 144.711 185.579 1.00 20.00 S ATOM 51795 SG CYS F 54 116.189 142.385 182.637 1.00 20.00 S ATOM 52084 SG CYS F 88 115.173 145.961 182.110 1.00 20.00 S ATOM 52108 SG CYS F 91 112.849 143.505 183.681 1.00 20.00 S Time building chain proxies: 29.79, per 1000 atoms: 0.40 Number of scatterers: 75273 At special positions: 0 Unit cell: (245.528, 304.298, 300.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 242 16.00 P 407 15.00 Mg 6 11.99 O 15318 8.00 N 13144 7.00 C 46149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.02 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 300 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 91 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 54 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 88 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 51 " pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 73 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 64 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 61 " pdb=" ZN R 400 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 81 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 148 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 104 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 153 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " Number of angles added : 39 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 309 helices and 81 sheets defined 48.7% alpha, 12.3% beta 105 base pairs and 179 stacking pairs defined. Time for finding SS restraints: 25.67 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 removed outlier: 5.083A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 4.587A pdb=" N THR A 156 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.583A pdb=" N LYS A 174 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 305 through 318 removed outlier: 4.230A pdb=" N THR A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 388 through 391 No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.774A pdb=" N ARG A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 640 Processing helix chain 'A' and resid 647 through 663 removed outlier: 6.138A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 671 through 689 removed outlier: 3.654A pdb=" N ILE A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 735 removed outlier: 3.515A pdb=" N THR A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.578A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 794 Processing helix chain 'A' and resid 806 through 836 removed outlier: 4.056A pdb=" N ARG A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 870 removed outlier: 4.046A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 908 through 924 removed outlier: 3.501A pdb=" N LEU A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1006 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.920A pdb=" N ARG A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1108 through 1126 removed outlier: 4.221A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1113 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A1123 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A1126 " --> pdb=" O LEU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1134 Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1329 through 1346 removed outlier: 3.838A pdb=" N SER A1341 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1352 Processing helix chain 'A' and resid 1354 through 1373 Processing helix chain 'A' and resid 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' Processing helix chain 'A' and resid 1392 through 1394 No H-bonds generated for 'chain 'A' and resid 1392 through 1394' Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1470 Processing helix chain 'A' and resid 1481 through 1483 No H-bonds generated for 'chain 'A' and resid 1481 through 1483' Processing helix chain 'A' and resid 1491 through 1495 Processing helix chain 'A' and resid 1497 through 1504 removed outlier: 4.564A pdb=" N HIS A1500 " --> pdb=" O ARG A1497 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A1503 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 4.452A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1541 through 1549 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 3.830A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1609 Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 4.454A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1671 Processing helix chain 'A' and resid 1673 through 1676 No H-bonds generated for 'chain 'A' and resid 1673 through 1676' Processing helix chain 'A' and resid 1688 through 1691 removed outlier: 4.478A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1688 through 1691' Processing helix chain 'A' and resid 1748 through 1761 Processing helix chain 'A' and resid 1794 through 1807 removed outlier: 3.897A pdb=" N ASN A1800 " --> pdb=" O PRO A1796 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1823 removed outlier: 3.781A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1844 Processing helix chain 'A' and resid 1896 through 1901 removed outlier: 4.300A pdb=" N GLY A1901 " --> pdb=" O VAL A1898 " (cutoff:3.500A) Processing helix chain 'A' and resid 1905 through 1923 Processing helix chain 'A' and resid 1941 through 1950 removed outlier: 3.930A pdb=" N LEU A1949 " --> pdb=" O GLU A1945 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP A1950 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1970 removed outlier: 4.448A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2020 through 2027 Processing helix chain 'A' and resid 2045 through 2067 removed outlier: 3.869A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2076 through 2084 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.749A pdb=" N MET C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.604A pdb=" N LEU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 170' Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.773A pdb=" N VAL C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.602A pdb=" N ASP C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.657A pdb=" N TYR C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 338 through 347 removed outlier: 4.814A pdb=" N ASP C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 345 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.827A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.274A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 583 through 587 removed outlier: 3.907A pdb=" N LYS C 587 " --> pdb=" O LYS C 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 587' Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix removed outlier: 4.330A pdb=" N LEU C 619 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 626 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 759 through 764 removed outlier: 3.898A pdb=" N ARG C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 785 through 803 removed outlier: 4.021A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 851 removed outlier: 3.955A pdb=" N ILE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix Processing helix chain 'C' and resid 870 through 883 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 909 through 911 No H-bonds generated for 'chain 'C' and resid 909 through 911' Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.760A pdb=" N ARG C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 117 Processing helix chain 'O' and resid 397 through 399 No H-bonds generated for 'chain 'O' and resid 397 through 399' Processing helix chain 'P' and resid 31 through 34 No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 40 through 42 No H-bonds generated for 'chain 'P' and resid 40 through 42' Processing helix chain 'P' and resid 63 through 82 removed outlier: 3.832A pdb=" N ALA P 68 " --> pdb=" O GLN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 93 removed outlier: 3.666A pdb=" N TYR P 93 " --> pdb=" O SER P 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 90 through 93' Processing helix chain 'P' and resid 159 through 163 Processing helix chain 'P' and resid 182 through 185 No H-bonds generated for 'chain 'P' and resid 182 through 185' Processing helix chain 'P' and resid 199 through 246 removed outlier: 3.745A pdb=" N LYS P 226 " --> pdb=" O LYS P 222 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU P 241 " --> pdb=" O LYS P 237 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN P 246 " --> pdb=" O LYS P 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 7 No H-bonds generated for 'chain 'Q' and resid 4 through 7' Processing helix chain 'Q' and resid 63 through 66 No H-bonds generated for 'chain 'Q' and resid 63 through 66' Processing helix chain 'Q' and resid 84 through 93 removed outlier: 3.519A pdb=" N ASP Q 88 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 115 removed outlier: 4.521A pdb=" N LEU Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 125 removed outlier: 3.946A pdb=" N ILE Q 125 " --> pdb=" O GLY Q 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 121 through 125' Processing helix chain 'Q' and resid 216 through 226 Processing helix chain 'Q' and resid 256 through 263 Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 55 through 58 No H-bonds generated for 'chain 'R' and resid 55 through 58' Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 74 through 77 No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 84 through 86 No H-bonds generated for 'chain 'R' and resid 84 through 86' Processing helix chain 'R' and resid 96 through 104 removed outlier: 5.316A pdb=" N LEU R 104 " --> pdb=" O GLY R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 145 Processing helix chain 'R' and resid 153 through 167 removed outlier: 4.378A pdb=" N ARG R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 199 Processing helix chain 'R' and resid 210 through 217 removed outlier: 4.653A pdb=" N ASP R 213 " --> pdb=" O LYS R 210 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG R 216 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 260 removed outlier: 3.618A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 19 Processing helix chain 'S' and resid 128 through 130 No H-bonds generated for 'chain 'S' and resid 128 through 130' Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'T' and resid 14 through 34 removed outlier: 4.124A pdb=" N GLU T 17 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS T 18 " --> pdb=" O GLY T 15 " (cutoff:3.500A) Proline residue: T 21 - end of helix removed outlier: 3.732A pdb=" N ASP T 25 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE T 28 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG T 31 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN T 34 " --> pdb=" O ARG T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 68 removed outlier: 3.590A pdb=" N ILE T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 84 Processing helix chain 'T' and resid 89 through 96 Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 126 through 136 removed outlier: 3.770A pdb=" N GLU T 131 " --> pdb=" O ALA T 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 31 Proline residue: Z 27 - end of helix Processing helix chain 'Z' and resid 37 through 46 Processing helix chain 'Z' and resid 53 through 66 Processing helix chain 'Z' and resid 71 through 86 Proline residue: Z 74 - end of helix removed outlier: 3.615A pdb=" N SER Z 77 " --> pdb=" O PRO Z 74 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Z 83 " --> pdb=" O ILE Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 108 Processing helix chain 'Z' and resid 111 through 126 Processing helix chain 'Z' and resid 132 through 144 Processing helix chain 'Z' and resid 148 through 165 removed outlier: 5.529A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 183 removed outlier: 3.634A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 183 " --> pdb=" O TYR Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 203 removed outlier: 3.634A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE Z 198 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN Z 202 " --> pdb=" O PHE Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 240 Processing helix chain 'Z' and resid 286 through 300 removed outlier: 3.658A pdb=" N PHE Z 291 " --> pdb=" O ASN Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 308 through 315 Processing helix chain 'Z' and resid 321 through 335 removed outlier: 4.317A pdb=" N VAL Z 325 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 353 removed outlier: 4.241A pdb=" N PHE Z 353 " --> pdb=" O ARG Z 349 " (cutoff:3.500A) Processing helix chain 'Z' and resid 355 through 375 removed outlier: 4.568A pdb=" N ILE Z 373 " --> pdb=" O TYR Z 369 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU Z 374 " --> pdb=" O THR Z 370 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP Z 375 " --> pdb=" O GLN Z 371 " (cutoff:3.500A) Processing helix chain 'Z' and resid 378 through 393 removed outlier: 3.666A pdb=" N ARG Z 382 " --> pdb=" O THR Z 378 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE Z 383 " --> pdb=" O ASP Z 379 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Z 386 " --> pdb=" O ARG Z 382 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU Z 391 " --> pdb=" O PHE Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 399 through 404 removed outlier: 3.876A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 431 removed outlier: 4.089A pdb=" N ASN Z 429 " --> pdb=" O GLN Z 425 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU Z 430 " --> pdb=" O GLU Z 426 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU Z 431 " --> pdb=" O LEU Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 434 through 443 removed outlier: 3.540A pdb=" N LEU Z 438 " --> pdb=" O ASP Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 468 Processing helix chain 'Z' and resid 475 through 484 removed outlier: 3.694A pdb=" N ARG Z 480 " --> pdb=" O ASP Z 476 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 28 Processing helix chain 'c' and resid 33 through 39 removed outlier: 3.580A pdb=" N SER c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU c 39 " --> pdb=" O LYS c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 67 through 79 Processing helix chain 'c' and resid 86 through 91 Processing helix chain 'c' and resid 95 through 106 Processing helix chain 'c' and resid 146 through 159 Processing helix chain 'c' and resid 165 through 193 Processing helix chain 'c' and resid 233 through 248 Processing helix chain 'c' and resid 338 through 355 removed outlier: 3.785A pdb=" N UNK c 355 " --> pdb=" O UNK c 351 " (cutoff:3.500A) Processing helix chain 'c' and resid 359 through 363 Processing helix chain 'c' and resid 374 through 381 Processing helix chain 'c' and resid 385 through 400 removed outlier: 3.637A pdb=" N UNK c 390 " --> pdb=" O UNK c 386 " (cutoff:3.500A) Processing helix chain 'c' and resid 423 through 437 removed outlier: 3.595A pdb=" N UNK c 427 " --> pdb=" O UNK c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 468 removed outlier: 3.505A pdb=" N UNK c 450 " --> pdb=" O UNK c 446 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N UNK c 468 " --> pdb=" O UNK c 464 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 586 removed outlier: 3.596A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) Proline residue: c 504 - end of helix removed outlier: 4.514A pdb=" N SER c 515 " --> pdb=" O GLU c 511 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS c 516 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS c 526 " --> pdb=" O GLN c 522 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.687A pdb=" N GLN c 536 " --> pdb=" O PRO c 532 " (cutoff:3.500A) Proline residue: c 550 - end of helix removed outlier: 3.965A pdb=" N ILE c 553 " --> pdb=" O LEU c 549 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU c 554 " --> pdb=" O PRO c 550 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN c 556 " --> pdb=" O LEU c 552 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER c 572 " --> pdb=" O GLN c 568 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 577 " --> pdb=" O LEU c 573 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS c 578 " --> pdb=" O GLU c 574 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG c 579 " --> pdb=" O GLY c 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU c 580 " --> pdb=" O ARG c 576 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU c 584 " --> pdb=" O LEU c 580 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN c 585 " --> pdb=" O GLN c 581 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER c 586 " --> pdb=" O ALA c 582 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 60 removed outlier: 3.710A pdb=" N GLU d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS d 50 " --> pdb=" O TYR d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 77 Processing helix chain 'd' and resid 81 through 94 Processing helix chain 'd' and resid 99 through 111 removed outlier: 3.873A pdb=" N GLU d 109 " --> pdb=" O TYR d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 128 removed outlier: 3.756A pdb=" N MET d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER d 127 " --> pdb=" O ASN d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 146 removed outlier: 3.831A pdb=" N LEU d 146 " --> pdb=" O VAL d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 161 Processing helix chain 'd' and resid 166 through 178 removed outlier: 3.910A pdb=" N ARG d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.742A pdb=" N ARG d 186 " --> pdb=" O TRP d 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU d 187 " --> pdb=" O ASN d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 212 removed outlier: 3.534A pdb=" N GLU d 209 " --> pdb=" O TRP d 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 215 through 235 removed outlier: 3.507A pdb=" N SER d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE d 226 " --> pdb=" O TYR d 222 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR d 228 " --> pdb=" O LEU d 224 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASN d 234 " --> pdb=" O ALA d 230 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU d 235 " --> pdb=" O ASN d 231 " (cutoff:3.500A) Processing helix chain 'd' and resid 240 through 256 Processing helix chain 'd' and resid 260 through 272 Processing helix chain 'd' and resid 298 through 310 Processing helix chain 'd' and resid 317 through 332 Processing helix chain 'd' and resid 341 through 353 Processing helix chain 'd' and resid 361 through 368 removed outlier: 3.813A pdb=" N UNK d 366 " --> pdb=" O UNK d 362 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK d 367 " --> pdb=" O UNK d 363 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNK d 368 " --> pdb=" O UNK d 364 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 374 Processing helix chain 'd' and resid 380 through 389 Processing helix chain 'd' and resid 394 through 400 Processing helix chain 'd' and resid 413 through 423 removed outlier: 3.951A pdb=" N UNK d 418 " --> pdb=" O UNK d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 443 removed outlier: 3.502A pdb=" N UNK d 443 " --> pdb=" O UNK d 439 " (cutoff:3.500A) Processing helix chain 'd' and resid 454 through 462 Processing helix chain 'd' and resid 469 through 479 removed outlier: 3.676A pdb=" N UNK d 473 " --> pdb=" O UNK d 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK d 479 " --> pdb=" O UNK d 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 488 through 498 removed outlier: 3.671A pdb=" N UNK d 494 " --> pdb=" O UNK d 490 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N UNK d 498 " --> pdb=" O UNK d 494 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 515 Processing helix chain 'd' and resid 520 through 527 Processing helix chain 'd' and resid 539 through 550 Processing helix chain 'd' and resid 561 through 575 removed outlier: 3.693A pdb=" N UNK d 575 " --> pdb=" O UNK d 571 " (cutoff:3.500A) Processing helix chain 'd' and resid 585 through 594 Processing helix chain 'd' and resid 602 through 619 Processing helix chain 'd' and resid 626 through 640 Processing helix chain 'F' and resid 17 through 30 removed outlier: 4.385A pdb=" N LYS F 29 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 9 Processing helix chain 'G' and resid 19 through 41 Processing helix chain 'H' and resid 4 through 7 No H-bonds generated for 'chain 'H' and resid 4 through 7' Processing helix chain 'H' and resid 11 through 23 removed outlier: 4.815A pdb=" N GLN H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 17 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER H 22 " --> pdb=" O GLN H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 63 removed outlier: 4.374A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 95 Processing helix chain 'I' and resid 97 through 122 removed outlier: 3.575A pdb=" N ALA I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 189 Processing helix chain 'I' and resid 198 through 210 Processing helix chain 'v' and resid 67 through 70 No H-bonds generated for 'chain 'v' and resid 67 through 70' Processing helix chain 'v' and resid 75 through 87 Processing helix chain 'v' and resid 91 through 102 Processing helix chain 'v' and resid 107 through 119 Processing helix chain 'v' and resid 125 through 136 Processing helix chain 'v' and resid 140 through 151 removed outlier: 3.607A pdb=" N UNK v 146 " --> pdb=" O UNK v 142 " (cutoff:3.500A) Processing helix chain 'v' and resid 156 through 168 Processing helix chain 'v' and resid 172 through 182 Processing helix chain 'v' and resid 187 through 200 Processing helix chain 'v' and resid 205 through 217 Processing helix chain 'v' and resid 221 through 232 Processing helix chain 'v' and resid 237 through 249 Processing helix chain 'v' and resid 255 through 266 Processing helix chain 'v' and resid 270 through 282 removed outlier: 3.608A pdb=" N UNK v 276 " --> pdb=" O UNK v 272 " (cutoff:3.500A) Processing helix chain 'v' and resid 286 through 298 Processing helix chain 'v' and resid 302 through 314 Processing helix chain 'v' and resid 320 through 333 Processing helix chain 'v' and resid 338 through 350 Processing helix chain 'v' and resid 356 through 365 removed outlier: 3.585A pdb=" N UNK v 363 " --> pdb=" O UNK v 360 " (cutoff:3.500A) Processing helix chain 'v' and resid 369 through 381 Processing helix chain 'v' and resid 388 through 400 Processing helix chain 'v' and resid 404 through 414 Processing helix chain 'v' and resid 421 through 436 Processing helix chain 'v' and resid 441 through 458 removed outlier: 4.253A pdb=" N UNK v 457 " --> pdb=" O UNK v 453 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N UNK v 458 " --> pdb=" O UNK v 454 " (cutoff:3.500A) Processing helix chain 'v' and resid 464 through 482 Processing helix chain 'v' and resid 488 through 500 Processing helix chain 'v' and resid 505 through 523 Processing helix chain 'v' and resid 528 through 541 removed outlier: 3.538A pdb=" N UNK v 534 " --> pdb=" O UNK v 530 " (cutoff:3.500A) Processing helix chain 'v' and resid 547 through 559 removed outlier: 4.177A pdb=" N UNK v 556 " --> pdb=" O UNK v 553 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N UNK v 557 " --> pdb=" O UNK v 554 " (cutoff:3.500A) Processing helix chain 'v' and resid 570 through 578 removed outlier: 4.379A pdb=" N VAL v 577 " --> pdb=" O ALA v 573 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE v 578 " --> pdb=" O TYR v 574 " (cutoff:3.500A) Processing helix chain 'v' and resid 585 through 597 Processing helix chain 'v' and resid 602 through 635 Proline residue: v 613 - end of helix Proline residue: v 616 - end of helix removed outlier: 4.277A pdb=" N ILE v 619 " --> pdb=" O PHE v 615 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR v 621 " --> pdb=" O PRO v 617 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU v 622 " --> pdb=" O GLU v 618 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU v 626 " --> pdb=" O GLU v 622 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN v 635 " --> pdb=" O ALA v 631 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 652 Processing helix chain 'v' and resid 664 through 675 removed outlier: 4.047A pdb=" N ARG v 675 " --> pdb=" O VAL v 671 " (cutoff:3.500A) Processing helix chain 'v' and resid 680 through 688 Processing helix chain 'v' and resid 707 through 719 Processing helix chain 'v' and resid 723 through 733 removed outlier: 3.722A pdb=" N GLU v 727 " --> pdb=" O SER v 723 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN v 730 " --> pdb=" O ARG v 726 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU v 731 " --> pdb=" O GLU v 727 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 755 removed outlier: 4.291A pdb=" N UNK v 751 " --> pdb=" O UNK v 747 " (cutoff:3.500A) Processing helix chain 'v' and resid 760 through 772 Processing helix chain 'v' and resid 780 through 791 Processing helix chain 'v' and resid 798 through 817 Processing helix chain 'n' and resid 53 through 62 removed outlier: 4.061A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR n 62 " --> pdb=" O ARG n 58 " (cutoff:3.500A) Processing helix chain 'n' and resid 424 through 426 No H-bonds generated for 'chain 'n' and resid 424 through 426' Processing helix chain 'o' and resid 25 through 34 removed outlier: 3.725A pdb=" N GLN o 30 " --> pdb=" O SER o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 139 removed outlier: 3.723A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE o 96 " --> pdb=" O MET o 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU o 98 " --> pdb=" O GLU o 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR o 101 " --> pdb=" O LYS o 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER o 104 " --> pdb=" O SER o 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS o 107 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL o 122 " --> pdb=" O ALA o 118 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) Proline residue: o 138 - end of helix Processing helix chain 'p' and resid 25 through 34 removed outlier: 3.590A pdb=" N LYS p 33 " --> pdb=" O GLU p 29 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 141 removed outlier: 3.594A pdb=" N GLU p 94 " --> pdb=" O ALA p 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET p 128 " --> pdb=" O ALA p 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU p 132 " --> pdb=" O MET p 128 " (cutoff:3.500A) Proline residue: p 138 - end of helix removed outlier: 3.648A pdb=" N SER p 141 " --> pdb=" O LEU p 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 34 Processing helix chain 'q' and resid 78 through 142 removed outlier: 3.655A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS q 97 " --> pdb=" O LEU q 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR q 101 " --> pdb=" O LYS q 97 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS q 108 " --> pdb=" O SER q 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS q 135 " --> pdb=" O ASN q 131 " (cutoff:3.500A) Proline residue: q 138 - end of helix Processing helix chain 'q' and resid 473 through 475 No H-bonds generated for 'chain 'q' and resid 473 through 475' Processing helix chain 'r' and resid 25 through 34 Processing helix chain 'r' and resid 78 through 138 removed outlier: 3.716A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU r 93 " --> pdb=" O ASP r 89 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG r 99 " --> pdb=" O ASN r 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR r 101 " --> pdb=" O LYS r 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU r 115 " --> pdb=" O THR r 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS r 120 " --> pdb=" O ARG r 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Proline residue: r 138 - end of helix Processing helix chain 't' and resid 14 through 31 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 83 through 102 removed outlier: 3.580A pdb=" N LYS t 94 " --> pdb=" O GLU t 90 " (cutoff:3.500A) Proline residue: t 96 - end of helix Processing helix chain 't' and resid 104 through 109 removed outlier: 4.054A pdb=" N SER t 109 " --> pdb=" O PRO t 105 " (cutoff:3.500A) Processing helix chain 't' and resid 112 through 174 removed outlier: 3.655A pdb=" N VAL t 117 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR t 120 " --> pdb=" O ILE t 116 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL t 127 " --> pdb=" O HIS t 123 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP t 129 " --> pdb=" O GLU t 125 " (cutoff:3.500A) Proline residue: t 133 - end of helix removed outlier: 3.740A pdb=" N ARG t 148 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU t 155 " --> pdb=" O CYS t 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG t 172 " --> pdb=" O LEU t 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 15 No H-bonds generated for 'chain 'k' and resid 13 through 15' Processing helix chain 'i' and resid 13 through 23 Processing helix chain 'i' and resid 84 through 86 No H-bonds generated for 'chain 'i' and resid 84 through 86' Processing helix chain 'h' and resid 15 through 21 Processing helix chain 'h' and resid 75 through 77 No H-bonds generated for 'chain 'h' and resid 75 through 77' Processing helix chain 'l' and resid 6 through 14 Processing helix chain 'm' and resid 3 through 9 Processing helix chain 'm' and resid 103 through 107 Processing helix chain 'g' and resid 16 through 28 Processing helix chain 'g' and resid 32 through 40 Processing helix chain 's' and resid 13 through 15 No H-bonds generated for 'chain 's' and resid 13 through 15' Processing helix chain 'u' and resid 13 through 23 Processing helix chain 'u' and resid 84 through 86 No H-bonds generated for 'chain 'u' and resid 84 through 86' Processing helix chain 'w' and resid 15 through 21 Processing helix chain 'w' and resid 75 through 77 No H-bonds generated for 'chain 'w' and resid 75 through 77' Processing helix chain 'y' and resid 6 through 14 Processing helix chain 'z' and resid 3 through 9 Processing helix chain 'z' and resid 103 through 107 Processing helix chain 'a' and resid 41 through 55 removed outlier: 4.195A pdb=" N THR a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 88 Processing helix chain 'b' and resid 5 through 10 removed outlier: 3.512A pdb=" N ASP b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 50 Processing helix chain 'b' and resid 111 through 119 removed outlier: 4.607A pdb=" N ARG b 116 " --> pdb=" O ASP b 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG b 119 " --> pdb=" O ARG b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 136 Processing helix chain 'b' and resid 140 through 147 Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 1247 through 1251 Processing sheet with id= D, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= E, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 6.802A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= G, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= H, first strand: chain 'A' and resid 1734 through 1739 removed outlier: 6.855A pdb=" N VAL A1773 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN A1737 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A1775 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A1739 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A1777 " --> pdb=" O ARG A1739 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1985 through 1990 removed outlier: 3.521A pdb=" N GLN A1985 " --> pdb=" O ILE A1893 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1880 " --> pdb=" O ASP A1853 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1859 through 1863 removed outlier: 4.062A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 320 through 322 removed outlier: 9.306A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 536 through 538 removed outlier: 6.607A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.996A pdb=" N LYS C 474 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= O, first strand: chain 'C' and resid 677 through 681 Processing sheet with id= P, first strand: chain 'C' and resid 774 through 776 removed outlier: 8.102A pdb=" N ILE C 775 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR C 818 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 928 through 931 removed outlier: 3.680A pdb=" N TYR C 931 " --> pdb=" O GLU C 863 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'O' and resid 187 through 190 Processing sheet with id= T, first strand: chain 'O' and resid 260 through 262 removed outlier: 3.530A pdb=" N ILE O 248 " --> pdb=" O LEU O 262 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 269 through 274 removed outlier: 6.923A pdb=" N SER O 284 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL O 272 " --> pdb=" O VAL O 282 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL O 282 " --> pdb=" O VAL O 272 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 314 through 316 Processing sheet with id= W, first strand: chain 'O' and resid 353 through 358 removed outlier: 6.744A pdb=" N GLY O 367 " --> pdb=" O ASN O 354 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU O 356 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE O 365 " --> pdb=" O LEU O 356 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE O 358 " --> pdb=" O VAL O 363 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL O 363 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL O 372 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 413 through 418 removed outlier: 3.866A pdb=" N SER O 422 " --> pdb=" O GLU O 418 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS O 427 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU O 131 " --> pdb=" O LYS O 427 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 164 through 167 removed outlier: 3.584A pdb=" N THR O 176 " --> pdb=" O VAL O 166 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Q' and resid 204 through 207 Processing sheet with id= AA, first strand: chain 'R' and resid 222 through 225 removed outlier: 4.061A pdb=" N CYS R 181 " --> pdb=" O VAL R 176 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 41 through 43 Processing sheet with id= AC, first strand: chain 'F' and resid 67 through 70 removed outlier: 4.895A pdb=" N TYR F 82 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 84 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'n' and resid 168 through 170 Processing sheet with id= AE, first strand: chain 'n' and resid 211 through 214 Processing sheet with id= AF, first strand: chain 'n' and resid 287 through 289 removed outlier: 3.531A pdb=" N ILE n 272 " --> pdb=" O TYR n 289 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'n' and resid 296 through 301 removed outlier: 6.923A pdb=" N SER n 311 " --> pdb=" O LEU n 297 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU n 299 " --> pdb=" O ILE n 309 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE n 309 " --> pdb=" O LEU n 299 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE n 308 " --> pdb=" O TRP n 320 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU n 321 " --> pdb=" O PRO n 327 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'n' and resid 342 through 344 Processing sheet with id= AI, first strand: chain 'n' and resid 381 through 383 removed outlier: 3.748A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP n 402 " --> pdb=" O PHE n 408 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE n 408 " --> pdb=" O ASP n 402 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'n' and resid 442 through 446 removed outlier: 3.866A pdb=" N LYS n 450 " --> pdb=" O GLY n 446 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP n 455 " --> pdb=" O VAL n 154 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL n 154 " --> pdb=" O ASP n 455 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'n' and resid 187 through 190 removed outlier: 3.585A pdb=" N ARG n 200 " --> pdb=" O ILE n 189 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'o' and resid 13 through 15 Processing sheet with id= AM, first strand: chain 'p' and resid 13 through 15 Processing sheet with id= AN, first strand: chain 'q' and resid 13 through 15 Processing sheet with id= AO, first strand: chain 'q' and resid 162 through 164 removed outlier: 3.610A pdb=" N GLN q 468 " --> pdb=" O CYS q 481 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'q' and resid 175 through 180 removed outlier: 6.255A pdb=" N TYR q 197 " --> pdb=" O ILE q 176 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS q 178 " --> pdb=" O PHE q 195 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE q 195 " --> pdb=" O LYS q 178 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG q 214 " --> pdb=" O LEU q 220 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU q 220 " --> pdb=" O ARG q 214 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'q' and resid 232 through 235 removed outlier: 5.637A pdb=" N ASN q 274 " --> pdb=" O PRO q 262 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'q' and resid 292 through 295 removed outlier: 3.594A pdb=" N TYR q 292 " --> pdb=" O ALA q 305 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'q' and resid 333 through 338 removed outlier: 6.250A pdb=" N TYR q 348 " --> pdb=" O SER q 334 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY q 336 " --> pdb=" O ALA q 346 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA q 346 " --> pdb=" O GLY q 336 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU q 338 " --> pdb=" O LEU q 344 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU q 344 " --> pdb=" O LEU q 338 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN q 358 " --> pdb=" O GLN q 364 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN q 364 " --> pdb=" O ASN q 358 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'q' and resid 379 through 382 removed outlier: 3.759A pdb=" N LEU q 409 " --> pdb=" O CYS q 399 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP q 401 " --> pdb=" O GLY q 407 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY q 407 " --> pdb=" O ASP q 401 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'q' and resid 457 through 459 Processing sheet with id= AV, first strand: chain 'r' and resid 13 through 16 removed outlier: 4.187A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'k' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'k' and resid 43 through 45 Processing sheet with id= AY, first strand: chain 'i' and resid 58 through 61 removed outlier: 3.544A pdb=" N GLN i 34 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU i 31 " --> pdb=" O GLN i 34 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLY i 36 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N ILE i 29 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG i 38 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL i 27 " --> pdb=" O ARG i 38 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'i' and resid 52 through 54 removed outlier: 3.847A pdb=" N VAL i 52 " --> pdb=" O LEU i 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU i 82 " --> pdb=" O VAL i 52 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU h 58 " --> pdb=" O THR h 67 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR h 67 " --> pdb=" O GLU h 58 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 71 through 73 removed outlier: 3.637A pdb=" N GLN h 52 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER h 44 " --> pdb=" O GLN h 52 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN h 54 " --> pdb=" O LEU h 42 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU h 42 " --> pdb=" O ASN h 54 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'h' and resid 28 through 31 removed outlier: 4.002A pdb=" N TYR h 80 " --> pdb=" O LYS h 30 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'j' and resid 23 through 25 Processing sheet with id= BE, first strand: chain 'j' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP j 41 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU j 29 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'l' and resid 69 through 73 removed outlier: 6.948A pdb=" N GLU l 22 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER l 20 " --> pdb=" O ILE l 72 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN l 43 " --> pdb=" O VAL l 34 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'l' and resid 47 through 50 Processing sheet with id= BH, first strand: chain 'm' and resid 80 through 82 removed outlier: 3.706A pdb=" N GLU m 13 " --> pdb=" O LEU m 29 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'm' and resid 84 through 87 removed outlier: 6.500A pdb=" N THR m 41 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU m 29 " --> pdb=" O THR m 41 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'g' and resid 87 through 91 removed outlier: 3.576A pdb=" N ARG g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'g' and resid 67 through 70 Processing sheet with id= BL, first strand: chain 's' and resid 77 through 83 removed outlier: 6.283A pdb=" N CYS s 48 " --> pdb=" O LEU s 82 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 's' and resid 43 through 45 Processing sheet with id= BN, first strand: chain 'u' and resid 58 through 61 removed outlier: 3.543A pdb=" N GLN u 34 " --> pdb=" O LEU u 31 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU u 31 " --> pdb=" O GLN u 34 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLY u 36 " --> pdb=" O ILE u 29 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N ILE u 29 " --> pdb=" O GLY u 36 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N ARG u 38 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL u 27 " --> pdb=" O ARG u 38 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'u' and resid 52 through 54 removed outlier: 3.847A pdb=" N VAL u 52 " --> pdb=" O LEU u 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU u 82 " --> pdb=" O VAL u 52 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'w' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU w 58 " --> pdb=" O THR w 67 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR w 67 " --> pdb=" O GLU w 58 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'w' and resid 71 through 73 removed outlier: 3.636A pdb=" N GLN w 52 " --> pdb=" O SER w 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER w 44 " --> pdb=" O GLN w 52 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN w 54 " --> pdb=" O LEU w 42 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU w 42 " --> pdb=" O ASN w 54 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'w' and resid 28 through 31 removed outlier: 4.003A pdb=" N TYR w 80 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'x' and resid 23 through 25 Processing sheet with id= BT, first strand: chain 'x' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP x 41 " --> pdb=" O LEU x 29 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU x 29 " --> pdb=" O ASP x 41 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'y' and resid 69 through 73 removed outlier: 6.949A pdb=" N GLU y 22 " --> pdb=" O LYS y 70 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE y 72 " --> pdb=" O SER y 20 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER y 20 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN y 43 " --> pdb=" O VAL y 34 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'y' and resid 47 through 50 Processing sheet with id= BW, first strand: chain 'z' and resid 80 through 82 removed outlier: 3.706A pdb=" N GLU z 13 " --> pdb=" O LEU z 29 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'z' and resid 84 through 87 removed outlier: 6.501A pdb=" N THR z 41 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU z 29 " --> pdb=" O THR z 41 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 53 through 55 removed outlier: 3.577A pdb=" N ARG e 89 " --> pdb=" O GLU e 74 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 67 through 70 Processing sheet with id= CA, first strand: chain 'e' and resid 45 through 48 removed outlier: 3.637A pdb=" N VAL e 103 " --> pdb=" O SER e 47 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'a' and resid 72 through 74 Processing sheet with id= CC, first strand: chain 'b' and resid 13 through 15 removed outlier: 7.106A pdb=" N ILE b 56 " --> pdb=" O LEU b 36 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR b 78 " --> pdb=" O LEU b 57 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN b 100 " --> pdb=" O LEU b 79 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN b 126 " --> pdb=" O LEU b 101 " (cutoff:3.500A) 3037 hydrogen bonds defined for protein. 8424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 105 basepair parallelities 179 stacking parallelities Total time for adding SS restraints: 41.71 Time building geometry restraints manager: 27.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.56: 75978 1.56 - 1.92: 1250 1.92 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 77229 Sorted by residual: bond pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 1.335 2.990 -1.654 1.97e-02 2.58e+03 7.05e+03 bond pdb=" CB CYS n 399 " pdb=" SG CYS n 399 " ideal model delta sigma weight residual 1.808 1.408 0.400 3.30e-02 9.18e+02 1.47e+02 bond pdb=" CB CYS n 444 " pdb=" SG CYS n 444 " ideal model delta sigma weight residual 1.808 1.430 0.378 3.30e-02 9.18e+02 1.31e+02 bond pdb=" CA ASP b 69 " pdb=" CB ASP b 69 " ideal model delta sigma weight residual 1.532 1.382 0.150 1.42e-02 4.96e+03 1.12e+02 bond pdb=" CB CYS n 454 " pdb=" SG CYS n 454 " ideal model delta sigma weight residual 1.808 1.478 0.330 3.30e-02 9.18e+02 9.98e+01 ... (remaining 77224 not shown) Histogram of bond angle deviations from ideal: 77.47 - 90.30: 3 90.30 - 103.13: 1488 103.13 - 115.96: 52575 115.96 - 128.79: 51336 128.79 - 141.62: 865 Bond angle restraints: 106267 Sorted by residual: angle pdb=" O PRO A 483 " pdb=" C PRO A 483 " pdb=" N PHE A 484 " ideal model delta sigma weight residual 122.64 77.47 45.17 1.35e+00 5.49e-01 1.12e+03 angle pdb=" O ALA q 247 " pdb=" C ALA q 247 " pdb=" N ARG q 256 " ideal model delta sigma weight residual 122.59 84.56 38.03 1.33e+00 5.65e-01 8.17e+02 angle pdb=" O3' C M 502 " pdb=" P A M 503 " pdb=" O5' A M 503 " ideal model delta sigma weight residual 104.00 79.95 24.05 1.50e+00 4.44e-01 2.57e+02 angle pdb=" N PRO b 44 " pdb=" CA PRO b 44 " pdb=" CB PRO b 44 " ideal model delta sigma weight residual 103.23 113.89 -10.66 6.70e-01 2.23e+00 2.53e+02 angle pdb=" C ALA q 247 " pdb=" N ARG q 256 " pdb=" CA ARG q 256 " ideal model delta sigma weight residual 120.17 141.06 -20.89 1.54e+00 4.22e-01 1.84e+02 ... (remaining 106262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 46014 35.81 - 71.63: 1346 71.63 - 107.44: 143 107.44 - 143.25: 28 143.25 - 179.07: 19 Dihedral angle restraints: 47550 sinusoidal: 21273 harmonic: 26277 Sorted by residual: dihedral pdb=" CA GLY n 67 " pdb=" C GLY n 67 " pdb=" N PRO n 68 " pdb=" CA PRO n 68 " ideal model delta harmonic sigma weight residual -180.00 -50.95 -129.05 0 5.00e+00 4.00e-02 6.66e+02 dihedral pdb=" CA ALA l 81 " pdb=" C ALA l 81 " pdb=" N PRO l 82 " pdb=" CA PRO l 82 " ideal model delta harmonic sigma weight residual -180.00 -52.75 -127.25 0 5.00e+00 4.00e-02 6.48e+02 dihedral pdb=" CA ALA y 81 " pdb=" C ALA y 81 " pdb=" N PRO y 82 " pdb=" CA PRO y 82 " ideal model delta harmonic sigma weight residual -180.00 -52.77 -127.23 0 5.00e+00 4.00e-02 6.47e+02 ... (remaining 47547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 11653 0.114 - 0.228: 876 0.228 - 0.342: 107 0.342 - 0.457: 10 0.457 - 0.571: 3 Chirality restraints: 12649 Sorted by residual: chirality pdb=" CA LYS e 82 " pdb=" N LYS e 82 " pdb=" C LYS e 82 " pdb=" CB LYS e 82 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CA LYS g 82 " pdb=" N LYS g 82 " pdb=" C LYS g 82 " pdb=" CB LYS g 82 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CA ILE Z 123 " pdb=" N ILE Z 123 " pdb=" C ILE Z 123 " pdb=" CB ILE Z 123 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 12646 not shown) Planarity restraints: 12082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA q 247 " 0.167 2.00e-02 2.50e+03 2.29e-01 5.23e+02 pdb=" C ALA q 247 " -0.387 2.00e-02 2.50e+03 pdb=" O ALA q 247 " 0.171 2.00e-02 2.50e+03 pdb=" N ARG q 256 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 483 " 0.116 2.00e-02 2.50e+03 1.67e-01 2.79e+02 pdb=" C PRO A 483 " -0.288 2.00e-02 2.50e+03 pdb=" O PRO A 483 " 0.072 2.00e-02 2.50e+03 pdb=" N PHE A 484 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Z 227 " -0.121 2.00e-02 2.50e+03 6.63e-02 8.78e+01 pdb=" CG TYR Z 227 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR Z 227 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR Z 227 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR Z 227 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR Z 227 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR Z 227 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR Z 227 " -0.103 2.00e-02 2.50e+03 ... (remaining 12079 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 35 2.08 - 2.79: 17095 2.79 - 3.49: 105975 3.49 - 4.20: 177847 4.20 - 4.90: 295232 Nonbonded interactions: 596184 Sorted by model distance: nonbonded pdb=" O ARG A 488 " pdb=" OD1 ASP C 416 " model vdw 1.378 3.040 nonbonded pdb=" O2' A M 501 " pdb=" P G N 100 " model vdw 1.612 3.400 nonbonded pdb=" CA GLU Z 192 " pdb=" OE2 GLU Z 195 " model vdw 1.699 3.470 nonbonded pdb=" O ALA Q 212 " pdb=" NH2 ARG R 237 " model vdw 1.707 2.520 nonbonded pdb=" OP2 U E 21 " pdb=" OG SER n 54 " model vdw 1.727 2.440 ... (remaining 596179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'h' selection = chain 'w' } ncs_group { reference = chain 'i' selection = chain 'u' } ncs_group { reference = chain 'j' selection = chain 'x' } ncs_group { reference = (chain 'k' and (resid 6 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 102)) selection = chain 's' } ncs_group { reference = chain 'l' selection = chain 'y' } ncs_group { reference = chain 'm' selection = chain 'z' } ncs_group { reference = (chain 'o' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'p' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 through 6 \ 3 or (resid 64 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 139)) selection = (chain 'r' and (resid 1 through 52 or resid 57 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.050 Extract box with map and model: 15.980 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 190.370 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.510 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 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 : 0.012 1.654 77229 Z= 0.779 Angle : 1.249 45.166 106267 Z= 0.768 Chirality : 0.067 0.571 12649 Planarity : 0.007 0.229 12082 Dihedral : 16.169 179.068 30332 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.73 % Favored : 91.22 % Rotamer: Outliers : 2.77 % Allowed : 3.70 % Favored : 93.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.04 % Twisted Proline : 2.34 % Twisted General : 0.34 % 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: -3.71 (0.08), residues: 7810 helix: -2.55 (0.07), residues: 3086 sheet: -1.98 (0.13), residues: 1111 loop : -2.45 (0.09), residues: 3613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP Z 18 HIS 0.026 0.002 HIS A1431 PHE 0.093 0.003 PHE Z 102 TYR 0.121 0.004 TYR Z 227 ARG 0.026 0.001 ARG Z 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15620 Ramachandran restraints generated. 7810 Oldfield, 0 Emsley, 7810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 7273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1729 time to evaluate : 7.373 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 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