Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 07:39:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esr_24422/04_2023/8esr_24422.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2372 5.49 5 S 156 5.16 5 C 64065 2.51 5 N 21708 2.21 5 O 28460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "V GLU 123": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 63": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 104": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "i GLU 86": "OE1" <-> "OE2" Residue "k ASP 50": "OD1" <-> "OD2" Residue "m ASP 114": "OD1" <-> "OD2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "o GLU 152": "OE1" <-> "OE2" Residue "o GLU 183": "OE1" <-> "OE2" Residue "o GLU 188": "OE1" <-> "OE2" Residue "r GLU 5": "OE1" <-> "OE2" Residue "r GLU 8": "OE1" <-> "OE2" Residue "r GLU 9": "OE1" <-> "OE2" Residue "r GLU 22": "OE1" <-> "OE2" Residue "r GLU 52": "OE1" <-> "OE2" Residue "r GLU 69": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v GLU 143": "OE1" <-> "OE2" Residue "v TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 177": "OE1" <-> "OE2" Residue "w GLU 451": "OE1" <-> "OE2" Residue "w GLU 680": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 116762 Number of models: 1 Model: "" Number of chains: 57 Chain: "1" Number of atoms: 45883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2143, 45883 Classifications: {'RNA': 2143} Modifications used: {'rna2p_pur': 228, 'rna2p_pyr': 137, 'rna3p_pur': 978, 'rna3p_pyr': 800} Link IDs: {'rna2p': 364, 'rna3p': 1778} Chain breaks: 42 Chain: "2" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3189 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 60} Link IDs: {'rna2p': 27, 'rna3p': 122} Chain breaks: 2 Chain: "6" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1674 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 15, 'rna3p_pur': 26, 'rna3p_pyr': 24} Link IDs: {'rna2p': 29, 'rna3p': 49} Chain breaks: 3 Chain: "7" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 214 Chain: "8" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 187 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2662 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2795 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 340} Chain: "D" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3320 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 18, 'TRANS': 399} Chain breaks: 2 Chain: "E" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1213 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain breaks: 1 Chain: "F" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1745 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "G" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1607 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 1 Chain: "H" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "I" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2032 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 369} Link IDs: {'PTRANS': 10, 'TRANS': 398} Chain breaks: 8 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1342 Unresolved non-hydrogen angles: 1696 Unresolved non-hydrogen dihedrals: 1112 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 13, 'TYR:plan': 15, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 24, 'GLU:plan': 29, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 671 Chain: "J" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 574 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 207 Chain: "K" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 235} Chain breaks: 1 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1392 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 2 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1168 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain breaks: 2 Chain: "Q" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1032 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 729 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "S" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1401 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "U" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 484 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 97} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 164 Chain: "V" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 991 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "W" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1057 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "X" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1044 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 1 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "Z" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 662 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 209 Chain: "a" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 762 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 1780 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 317} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1148 Unresolved non-hydrogen angles: 1467 Unresolved non-hydrogen dihedrals: 947 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 15, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 595 Chain: "c" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 462 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "d" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 801 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "e" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 478 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 154 Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "k" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "l" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 860 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 759 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 8, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 336 Chain: "m" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4526 Classifications: {'peptide': 572} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 43, 'TRANS': 528} Chain breaks: 6 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3517 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 410} Chain breaks: 2 Chain: "o" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1138 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "p" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1357 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 5 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 830 Unresolved non-hydrogen angles: 1084 Unresolved non-hydrogen dihedrals: 707 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 9, 'ASP:plan': 21, 'PHE:plan': 10, 'GLU:plan': 6, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 432 Chain: "q" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1282 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 247} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 796 Unresolved non-hydrogen angles: 1016 Unresolved non-hydrogen dihedrals: 657 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 422 Chain: "r" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1081 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "t" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1948 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain: "u" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 714 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 80 Chain: "v" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 1 Chain: "w" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1462 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Chain: "y" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1097 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 607 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 328 Chain: "z" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "T" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "j" 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 94776 SG CYS j 19 129.765 139.313 172.108 1.00 29.83 S ATOM 94804 SG CYS j 22 132.340 140.137 169.351 1.00 32.76 S ATOM 94900 SG CYS j 34 130.821 136.758 169.504 1.00 11.52 S ATOM 94917 SG CYS j 37 133.194 137.866 172.340 1.00 8.67 S Time building chain proxies: 45.07, per 1000 atoms: 0.39 Number of scatterers: 116762 At special positions: 0 Unit cell: (244.86, 207.76, 321.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 156 16.00 P 2372 15.00 O 28460 8.00 N 21708 7.00 C 64065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.93 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: 45.05 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17552 Finding SS restraints... Secondary structure from input PDB file: 350 helices and 98 sheets defined 43.7% alpha, 15.7% beta 757 base pairs and 1357 stacking pairs defined. Time for finding SS restraints: 34.57 Creating SS restraints... Processing helix chain '7' and resid 483 through 499 Processing helix chain '7' and resid 509 through 517 Processing helix chain '7' and resid 550 through 569 Processing helix chain '7' and resid 574 through 589 Proline residue: 7 581 - end of helix Processing helix chain '7' and resid 602 through 623 Processing helix chain '7' and resid 629 through 637 removed outlier: 4.239A pdb=" N VAL 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 20 removed outlier: 4.018A pdb=" N ASN 8 20 " --> pdb=" O ALA 8 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.679A pdb=" N GLY C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.116A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 259 through 265 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 98 through 108 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.964A pdb=" N ARG D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.947A pdb=" N ALA D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 Proline residue: D 146 - end of helix Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.663A pdb=" N ASP D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.562A pdb=" N LEU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 279 through 290 removed outlier: 3.515A pdb=" N GLU D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 416 through 424 removed outlier: 4.292A pdb=" N HIS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 455 removed outlier: 3.798A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 483 through 503 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.584A pdb=" N ASN E 147 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 38 through 80 Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.846A pdb=" N ILE F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 4.060A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.975A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.499A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.603A pdb=" N LEU G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.185A pdb=" N LEU G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.808A pdb=" N LYS G 232 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 removed outlier: 4.034A pdb=" N THR G 256 " --> pdb=" O ALA G 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.982A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'I' and resid 224 through 234 Processing helix chain 'I' and resid 238 through 249 Processing helix chain 'I' and resid 255 through 272 Processing helix chain 'I' and resid 293 through 321 removed outlier: 3.741A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 347 Processing helix chain 'I' and resid 352 through 365 Processing helix chain 'I' and resid 372 through 387 Processing helix chain 'I' and resid 390 through 407 Processing helix chain 'I' and resid 412 through 418 removed outlier: 3.942A pdb=" N TYR I 416 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 422 Processing helix chain 'I' and resid 453 through 504 removed outlier: 3.662A pdb=" N LYS I 458 " --> pdb=" O LYS I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 519 Processing helix chain 'I' and resid 523 through 536 removed outlier: 3.761A pdb=" N LEU I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 570 Processing helix chain 'I' and resid 584 through 593 Processing helix chain 'I' and resid 593 through 598 Processing helix chain 'I' and resid 630 through 643 Processing helix chain 'I' and resid 650 through 663 removed outlier: 3.968A pdb=" N SER I 654 " --> pdb=" O SER I 650 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG I 658 " --> pdb=" O SER I 654 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 659 " --> pdb=" O PHE I 655 " (cutoff:3.500A) Processing helix chain 'I' and resid 667 through 680 removed outlier: 3.666A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 686 through 690 removed outlier: 4.180A pdb=" N SER I 689 " --> pdb=" O SER I 686 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 728 removed outlier: 3.968A pdb=" N ASN I 728 " --> pdb=" O PHE I 724 " (cutoff:3.500A) Processing helix chain 'I' and resid 731 through 742 removed outlier: 4.242A pdb=" N SER I 735 " --> pdb=" O SER I 731 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN I 736 " --> pdb=" O PRO I 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 159 removed outlier: 3.963A pdb=" N GLU J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 208 removed outlier: 3.669A pdb=" N LYS J 183 " --> pdb=" O ASP J 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 27 removed outlier: 3.753A pdb=" N GLU K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 106 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.568A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.746A pdb=" N PHE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'K' and resid 174 through 188 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 232 through 234 No H-bonds generated for 'chain 'K' and resid 232 through 234' Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 88 through 93 removed outlier: 4.283A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.524A pdb=" N GLU L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.191A pdb=" N GLN M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.612A pdb=" N ASN N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 172 removed outlier: 3.525A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 31 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 60 Processing helix chain 'O' and resid 66 through 70 Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 102 Processing helix chain 'O' and resid 110 through 115 removed outlier: 3.983A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 124 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 147 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.849A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 192 removed outlier: 4.421A pdb=" N GLN O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU O 192 " --> pdb=" O VAL O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 196 Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.361A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.599A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 178 removed outlier: 3.583A pdb=" N ALA P 173 " --> pdb=" O LEU P 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 Processing helix chain 'Q' and resid 54 through 58 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 92 through 112 Processing helix chain 'R' and resid 116 through 128 Processing helix chain 'R' and resid 134 through 145 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 141 Processing helix chain 'U' and resid 16 through 23 Processing helix chain 'U' and resid 26 through 38 Processing helix chain 'U' and resid 70 through 86 Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.742A pdb=" N ASP W 59 " --> pdb=" O ARG W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.789A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU W 95 " --> pdb=" O LYS W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.792A pdb=" N VAL W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 205 Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 12 through 16 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 77 Processing helix chain 'X' and resid 90 through 103 Processing helix chain 'X' and resid 130 through 139 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.193A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 76 No H-bonds generated for 'chain 'Y' and resid 74 through 76' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Z' and resid 58 through 67 Processing helix chain 'Z' and resid 89 through 93 Processing helix chain 'Z' and resid 97 through 103 Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 77 through 82 removed outlier: 3.896A pdb=" N LEU a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 130 through 140 Processing helix chain 'b' and resid 14 through 30 Processing helix chain 'b' and resid 39 through 69 removed outlier: 3.515A pdb=" N PHE b 69 " --> pdb=" O ILE b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 88 through 119 removed outlier: 4.021A pdb=" N TYR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 144 Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.536A pdb=" N GLU b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.637A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 275 Processing helix chain 'b' and resid 275 through 280 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 399 through 407 Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 440 through 445 Processing helix chain 'c' and resid 23 through 35 removed outlier: 3.625A pdb=" N LYS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 51 Processing helix chain 'c' and resid 63 through 78 Processing helix chain 'c' and resid 87 through 96 Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.569A pdb=" N LEU e 81 " --> pdb=" O SER e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 removed outlier: 3.974A pdb=" N ASN e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 43 Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.627A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.517A pdb=" N LYS g 70 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 107 Processing helix chain 'h' and resid 4 through 10 Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.128A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 101 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 removed outlier: 3.513A pdb=" N LYS i 28 " --> pdb=" O SER i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.638A pdb=" N GLY i 47 " --> pdb=" O ARG i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 61 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 98 Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.894A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 74 Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 Processing helix chain 'l' and resid 5 through 21 removed outlier: 3.546A pdb=" N GLU l 14 " --> pdb=" O LYS l 10 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 29 removed outlier: 3.984A pdb=" N LEU l 27 " --> pdb=" O ASN l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 58 removed outlier: 3.910A pdb=" N SER l 57 " --> pdb=" O LYS l 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL l 58 " --> pdb=" O MET l 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 92 removed outlier: 3.989A pdb=" N GLN l 91 " --> pdb=" O ASP l 87 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR l 92 " --> pdb=" O TYR l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 110 removed outlier: 3.910A pdb=" N MET l 105 " --> pdb=" O SER l 101 " (cutoff:3.500A) Proline residue: l 106 - end of helix Processing helix chain 'l' and resid 149 through 154 Processing helix chain 'l' and resid 170 through 173 Processing helix chain 'm' and resid 133 through 137 removed outlier: 3.829A pdb=" N LYS m 137 " --> pdb=" O ILE m 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 146 through 156 Processing helix chain 'm' and resid 176 through 188 Processing helix chain 'm' and resid 221 through 226 removed outlier: 3.677A pdb=" N ARG m 224 " --> pdb=" O PRO m 221 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA m 226 " --> pdb=" O ARG m 223 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 260 removed outlier: 3.665A pdb=" N ALA m 254 " --> pdb=" O SER m 250 " (cutoff:3.500A) Processing helix chain 'm' and resid 328 through 343 removed outlier: 3.540A pdb=" N TYR m 341 " --> pdb=" O CYS m 337 " (cutoff:3.500A) Processing helix chain 'm' and resid 355 through 359 Processing helix chain 'm' and resid 483 through 492 removed outlier: 3.900A pdb=" N ILE m 487 " --> pdb=" O SER m 483 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU m 488 " --> pdb=" O ASP m 484 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 40 Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 73 Processing helix chain 'n' and resid 75 through 97 removed outlier: 3.901A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 109 Processing helix chain 'n' and resid 115 through 123 Processing helix chain 'n' and resid 125 through 132 removed outlier: 3.567A pdb=" N ASP n 132 " --> pdb=" O ASP n 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 133 through 144 Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 215 through 242 Processing helix chain 'n' and resid 250 through 256 Processing helix chain 'n' and resid 258 through 261 Processing helix chain 'n' and resid 365 through 376 removed outlier: 4.357A pdb=" N PHE n 371 " --> pdb=" O PHE n 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 384 through 387 Processing helix chain 'n' and resid 420 through 431 removed outlier: 4.144A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR n 425 " --> pdb=" O PRO n 421 " (cutoff:3.500A) Processing helix chain 'n' and resid 550 through 559 Processing helix chain 'n' and resid 560 through 565 Processing helix chain 'n' and resid 568 through 571 Processing helix chain 'n' and resid 572 through 598 removed outlier: 4.529A pdb=" N ASN n 578 " --> pdb=" O SER n 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN n 580 " --> pdb=" O LEU n 576 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG n 591 " --> pdb=" O ASN n 587 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN n 592 " --> pdb=" O ASN n 588 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 129 removed outlier: 4.022A pdb=" N GLN o 127 " --> pdb=" O MET o 123 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 removed outlier: 3.583A pdb=" N ALA o 159 " --> pdb=" O SER o 155 " (cutoff:3.500A) Processing helix chain 'o' and resid 202 through 212 Processing helix chain 'o' and resid 216 through 225 Processing helix chain 'o' and resid 226 through 238 removed outlier: 3.777A pdb=" N LYS o 234 " --> pdb=" O LYS o 230 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS o 237 " --> pdb=" O LEU o 233 " (cutoff:3.500A) Processing helix chain 'q' and resid 275 through 287 Processing helix chain 'q' and resid 313 through 319 Processing helix chain 'q' and resid 325 through 336 Proline residue: q 331 - end of helix Processing helix chain 'q' and resid 351 through 362 Processing helix chain 'q' and resid 373 through 388 removed outlier: 3.533A pdb=" N ALA q 379 " --> pdb=" O ALA q 375 " (cutoff:3.500A) Processing helix chain 'q' and resid 401 through 406 Processing helix chain 'q' and resid 441 through 458 Processing helix chain 'q' and resid 476 through 491 removed outlier: 4.162A pdb=" N ALA q 482 " --> pdb=" O ASP q 478 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL q 483 " --> pdb=" O GLU q 479 " (cutoff:3.500A) Processing helix chain 'q' and resid 517 through 522 Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.616A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN r 40 " --> pdb=" O SER r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 72 removed outlier: 3.610A pdb=" N ARG r 71 " --> pdb=" O GLN r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 25 Processing helix chain 't' and resid 25 through 45 Processing helix chain 't' and resid 53 through 76 removed outlier: 3.796A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 112 Processing helix chain 't' and resid 126 through 136 Processing helix chain 't' and resid 146 through 158 Processing helix chain 't' and resid 171 through 180 removed outlier: 4.185A pdb=" N ILE t 175 " --> pdb=" O ASP t 171 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 183 No H-bonds generated for 'chain 't' and resid 181 through 183' Processing helix chain 't' and resid 186 through 197 Processing helix chain 't' and resid 200 through 208 Processing helix chain 't' and resid 219 through 225 Processing helix chain 't' and resid 240 through 247 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.794A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG u 96 " --> pdb=" O ASN u 92 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 removed outlier: 3.625A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 120 through 125 removed outlier: 3.713A pdb=" N ASP v 125 " --> pdb=" O ASP v 121 " (cutoff:3.500A) Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.956A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 185 removed outlier: 3.544A pdb=" N ASP v 185 " --> pdb=" O SER v 181 " (cutoff:3.500A) Processing helix chain 'v' and resid 194 through 207 removed outlier: 3.829A pdb=" N ALA v 207 " --> pdb=" O ILE v 203 " (cutoff:3.500A) Processing helix chain 'w' and resid 447 through 472 Processing helix chain 'w' and resid 474 through 483 Processing helix chain 'w' and resid 623 through 636 Processing helix chain 'w' and resid 639 through 647 Processing helix chain 'w' and resid 660 through 671 removed outlier: 4.326A pdb=" N GLU w 666 " --> pdb=" O TRP w 662 " (cutoff:3.500A) Processing helix chain 'w' and resid 678 through 690 Processing helix chain 'w' and resid 696 through 717 removed outlier: 4.353A pdb=" N ALA w 703 " --> pdb=" O LYS w 699 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN w 704 " --> pdb=" O VAL w 700 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS w 707 " --> pdb=" O ALA w 703 " (cutoff:3.500A) Processing helix chain 'w' and resid 762 through 766 Processing helix chain 'w' and resid 785 through 796 removed outlier: 4.191A pdb=" N ASP w 789 " --> pdb=" O ARG w 785 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 16 removed outlier: 3.793A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 31 through 43 removed outlier: 4.293A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 88 through 100 removed outlier: 3.988A pdb=" N LYS z 100 " --> pdb=" O LYS z 96 " (cutoff:3.500A) Processing helix chain 'z' and resid 104 through 117 removed outlier: 3.636A pdb=" N PHE z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.700A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 230 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 244 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 232 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.700A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 221 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU A 204 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 202 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 200 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU A 149 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.149A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.149A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.799A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 23 removed outlier: 4.417A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA9, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.490A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 129 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 273 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.755A pdb=" N VAL D 339 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N CYS D 392 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL D 341 " --> pdb=" O CYS D 392 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D 408 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE D 440 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN D 410 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR D 315 " --> pdb=" O PHE D 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.832A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 82 through 84 removed outlier: 4.019A pdb=" N TYR F 82 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL T 141 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL F 84 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 212 through 213 removed outlier: 3.996A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG F 238 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR F 143 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AB8, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.028A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 130 through 134 removed outlier: 5.896A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC3, first strand: chain 'K' and resid 198 through 205 removed outlier: 5.925A pdb=" N SER K 198 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR K 59 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N MET K 200 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU K 57 " --> pdb=" O MET K 200 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS K 202 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU K 55 " --> pdb=" O LYS K 202 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY K 204 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA K 237 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASN K 253 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE K 239 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 72 through 74 removed outlier: 3.627A pdb=" N PHE K 191 " --> pdb=" O TYR K 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.270A pdb=" N ALA K 87 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG K 113 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AC7, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC8, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC9, first strand: chain 'M' and resid 49 through 52 removed outlier: 6.601A pdb=" N ARG M 36 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 32 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP M 40 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE M 28 " --> pdb=" O ASP M 40 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE M 61 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU M 15 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR M 59 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.451A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.204A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL O 34 " --> pdb=" O GLN O 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AD4, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.590A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD6, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.310A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD8, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD9, first strand: chain 'S' and resid 55 through 62 removed outlier: 5.055A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 89 through 95 removed outlier: 4.090A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 51 through 53 removed outlier: 3.944A pdb=" N LEU U 103 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL U 100 " --> pdb=" O THR U 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR U 96 " --> pdb=" O VAL U 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 39 through 40 Processing sheet with id=AE4, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AE5, first strand: chain 'V' and resid 24 through 27 removed outlier: 6.344A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 87 through 88 removed outlier: 5.871A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 136 through 137 removed outlier: 3.634A pdb=" N ILE W 137 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE W 185 " --> pdb=" O ILE W 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE9, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.208A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF2, first strand: chain 'Y' and resid 66 through 67 removed outlier: 6.857A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 69 through 73 removed outlier: 3.803A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 85 through 87 Processing sheet with id=AF5, first strand: chain 'Z' and resid 70 through 76 removed outlier: 7.999A pdb=" N HIS Z 40 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS Z 22 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS Z 21 " --> pdb=" O ILE Z 13 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AF7, first strand: chain 'a' and resid 100 through 102 Processing sheet with id=AF8, first strand: chain 'b' and resid 206 through 211 removed outlier: 3.578A pdb=" N PHE b 206 " --> pdb=" O ASP b 221 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR b 170 " --> pdb=" O ALA b 250 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 254 through 256 Processing sheet with id=AG1, first strand: chain 'c' and resid 36 through 38 removed outlier: 6.415A pdb=" N LYS c 36 " --> pdb=" O ILE c 107 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE c 56 " --> pdb=" O HIS c 82 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR c 84 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE c 58 " --> pdb=" O TYR c 84 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 53 through 56 removed outlier: 4.179A pdb=" N THR d 14 " --> pdb=" O VAL d 111 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 69 through 73 removed outlier: 5.868A pdb=" N LYS e 69 " --> pdb=" O ALA e 90 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU e 92 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE e 71 " --> pdb=" O GLU e 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.927A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG6, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.600A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 4 through 5 removed outlier: 4.242A pdb=" N VAL k 47 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA k 23 " --> pdb=" O THR k 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 36 through 40 removed outlier: 6.540A pdb=" N VAL l 44 " --> pdb=" O PHE l 70 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE l 68 " --> pdb=" O TYR l 46 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 113 through 114 removed outlier: 6.315A pdb=" N PHE l 143 " --> pdb=" O GLN l 166 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP l 168 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU l 141 " --> pdb=" O ASP l 168 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE l 133 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE l 143 " --> pdb=" O VAL l 131 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL l 131 " --> pdb=" O PHE l 143 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL l 145 " --> pdb=" O GLN l 129 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN l 129 " --> pdb=" O VAL l 145 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE l 97 " --> pdb=" O TYR l 134 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 118 through 119 removed outlier: 3.680A pdb=" N GLY m 118 " --> pdb=" O VAL m 165 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL m 165 " --> pdb=" O GLY m 118 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE m 164 " --> pdb=" O VAL m 173 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 345 through 348 Processing sheet with id=AH3, first strand: chain 'm' and resid 388 through 391 Processing sheet with id=AH4, first strand: chain 'm' and resid 454 through 457 removed outlier: 3.795A pdb=" N SER m 454 " --> pdb=" O ALA m 469 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA m 523 " --> pdb=" O PHE m 476 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 533 through 536 Processing sheet with id=AH6, first strand: chain 'm' and resid 576 through 581 removed outlier: 4.433A pdb=" N TYR m 595 " --> pdb=" O THR m 592 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL m 596 " --> pdb=" O THR m 609 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR m 609 " --> pdb=" O VAL m 596 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE m 598 " --> pdb=" O VAL m 607 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 617 through 622 Processing sheet with id=AH8, first strand: chain 'm' and resid 660 through 665 removed outlier: 5.853A pdb=" N VAL m 681 " --> pdb=" O ILE m 703 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE m 703 " --> pdb=" O VAL m 681 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL m 683 " --> pdb=" O LEU m 701 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'm' and resid 715 through 720 removed outlier: 6.827A pdb=" N ALA m 730 " --> pdb=" O LEU m 716 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR m 718 " --> pdb=" O PHE m 728 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE m 728 " --> pdb=" O THR m 718 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AI2, first strand: chain 'n' and resid 177 through 182 removed outlier: 5.395A pdb=" N LEU n 177 " --> pdb=" O GLU n 192 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU n 192 " --> pdb=" O LEU n 177 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'n' and resid 248 through 249 removed outlier: 4.119A pdb=" N LYS n 248 " --> pdb=" O GLU n 264 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU n 264 " --> pdb=" O LYS n 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'n' and resid 379 through 382 removed outlier: 6.452A pdb=" N THR n 357 " --> pdb=" O HIS n 401 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE n 403 " --> pdb=" O THR n 357 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE n 359 " --> pdb=" O ILE n 403 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS n 402 " --> pdb=" O ILE n 419 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'o' and resid 131 through 138 removed outlier: 3.790A pdb=" N ARG o 133 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR o 148 " --> pdb=" O SER o 137 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL o 106 " --> pdb=" O ILE o 181 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 96 through 102 removed outlier: 6.671A pdb=" N ILE p 430 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER p 100 " --> pdb=" O LEU p 428 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU p 428 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN p 427 " --> pdb=" O GLY p 423 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY p 423 " --> pdb=" O GLN p 427 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 107 through 112 Processing sheet with id=AI8, first strand: chain 'p' and resid 146 through 151 removed outlier: 6.573A pdb=" N ALA p 161 " --> pdb=" O LYS p 147 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA p 149 " --> pdb=" O LEU p 159 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU p 159 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP p 151 " --> pdb=" O SER p 157 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER p 157 " --> pdb=" O TRP p 151 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS p 166 " --> pdb=" O SER p 162 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR p 191 " --> pdb=" O HIS p 169 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL p 171 " --> pdb=" O LEU p 189 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU p 189 " --> pdb=" O VAL p 171 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 202 through 203 removed outlier: 3.533A pdb=" N ILE p 263 " --> pdb=" O ILE p 223 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'p' and resid 275 through 277 removed outlier: 4.109A pdb=" N ASP p 305 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP p 297 " --> pdb=" O ASN p 303 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN p 303 " --> pdb=" O ASP p 297 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'p' and resid 313 through 319 Processing sheet with id=AJ3, first strand: chain 'p' and resid 358 through 363 removed outlier: 6.814A pdb=" N VAL p 374 " --> pdb=" O SER p 359 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU p 361 " --> pdb=" O ALA p 372 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA p 372 " --> pdb=" O LEU p 361 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA p 363 " --> pdb=" O MET p 370 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET p 370 " --> pdb=" O ALA p 363 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR p 379 " --> pdb=" O SER p 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL p 382 " --> pdb=" O TYR p 393 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'q' and resid 288 through 292 removed outlier: 3.648A pdb=" N GLU q 305 " --> pdb=" O ASN q 289 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU q 291 " --> pdb=" O VAL q 303 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL q 303 " --> pdb=" O GLU q 291 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 392 through 395 removed outlier: 6.769A pdb=" N ILE q 367 " --> pdb=" O ILE q 393 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS q 395 " --> pdb=" O ILE q 367 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA q 369 " --> pdb=" O CYS q 395 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN q 370 " --> pdb=" O ASP q 345 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL q 413 " --> pdb=" O VAL q 469 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER q 471 " --> pdb=" O VAL q 413 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU q 415 " --> pdb=" O SER q 471 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY q 466 " --> pdb=" O LYS q 543 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS q 540 " --> pdb=" O VAL q 497 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 392 through 395 removed outlier: 6.769A pdb=" N ILE q 367 " --> pdb=" O ILE q 393 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS q 395 " --> pdb=" O ILE q 367 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA q 369 " --> pdb=" O CYS q 395 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN q 370 " --> pdb=" O ASP q 345 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL q 413 " --> pdb=" O VAL q 469 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER q 471 " --> pdb=" O VAL q 413 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU q 415 " --> pdb=" O SER q 471 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY q 466 " --> pdb=" O LYS q 543 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 510 through 511 Processing sheet with id=AJ8, first strand: chain 'r' and resid 180 through 184 removed outlier: 5.385A pdb=" N VAL r 199 " --> pdb=" O GLU r 221 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU r 221 " --> pdb=" O VAL r 199 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA r 256 " --> pdb=" O LYS r 180 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN r 182 " --> pdb=" O ALA r 256 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU r 258 " --> pdb=" O ASN r 182 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR r 184 " --> pdb=" O LEU r 258 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 't' and resid 211 through 212 removed outlier: 4.159A pdb=" N ASN t 119 " --> pdb=" O ARG t 94 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL t 140 " --> pdb=" O GLY t 235 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS t 237 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR t 142 " --> pdb=" O CYS t 237 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 't' and resid 159 through 162 removed outlier: 3.569A pdb=" N ILE t 162 " --> pdb=" O GLN t 165 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AK3, first strand: chain 'w' and resid 757 through 760 removed outlier: 6.184A pdb=" N THR w 757 " --> pdb=" O LYS w 780 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL w 782 " --> pdb=" O THR w 757 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL w 759 " --> pdb=" O VAL w 782 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'y' and resid 3 through 4 removed outlier: 5.975A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.633A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.508A pdb=" N CYS y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL y 97 " --> pdb=" O LEU y 70 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL y 72 " --> pdb=" O VAL y 97 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AK8, first strand: chain 'y' and resid 153 through 154 3314 hydrogen bonds defined for protein. 9468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1839 hydrogen bonds 2986 hydrogen bond angles 0 basepair planarities 757 basepair parallelities 1357 stacking parallelities Total time for adding SS restraints: 114.01 Time building geometry restraints manager: 48.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 30209 1.34 - 1.46: 41652 1.46 - 1.59: 46891 1.59 - 1.71: 4694 1.71 - 1.83: 255 Bond restraints: 123701 Sorted by residual: bond pdb=" CB GLU r 8 " pdb=" CG GLU r 8 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.49e+00 bond pdb=" CA CYS u 9 " pdb=" CB CYS u 9 " ideal model delta sigma weight residual 1.530 1.501 0.029 1.68e-02 3.54e+03 2.97e+00 bond pdb=" CA ASN u 45 " pdb=" C ASN u 45 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.08e-02 8.57e+03 2.44e+00 bond pdb=" CA GLU m 367 " pdb=" C GLU m 367 " ideal model delta sigma weight residual 1.527 1.509 0.018 1.21e-02 6.83e+03 2.27e+00 bond pdb=" CG1 ILE r 11 " pdb=" CD1 ILE r 11 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 ... (remaining 123696 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.73: 11289 104.73 - 112.07: 67675 112.07 - 119.41: 39362 119.41 - 126.74: 53387 126.74 - 134.08: 7210 Bond angle restraints: 178923 Sorted by residual: angle pdb=" N PRO a 67 " pdb=" CA PRO a 67 " pdb=" CB PRO a 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.47e+01 angle pdb=" N PRO m 372 " pdb=" CA PRO m 372 " pdb=" C PRO m 372 " ideal model delta sigma weight residual 112.47 101.22 11.25 2.06e+00 2.36e-01 2.98e+01 angle pdb=" N PRO m 370 " pdb=" CA PRO m 370 " pdb=" C PRO m 370 " ideal model delta sigma weight residual 112.47 103.02 9.45 2.06e+00 2.36e-01 2.10e+01 angle pdb=" N PHE m 371 " pdb=" CA PHE m 371 " pdb=" C PHE m 371 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.77e+01 angle pdb=" N VAL b 411 " pdb=" CA VAL b 411 " pdb=" C VAL b 411 " ideal model delta sigma weight residual 113.71 110.03 3.68 9.50e-01 1.11e+00 1.50e+01 ... (remaining 178918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 66851 35.97 - 71.94: 2261 71.94 - 107.90: 178 107.90 - 143.87: 20 143.87 - 179.84: 28 Dihedral angle restraints: 69338 sinusoidal: 42392 harmonic: 26946 Sorted by residual: dihedral pdb=" C4' A 1 644 " pdb=" C3' A 1 644 " pdb=" C2' A 1 644 " pdb=" C1' A 1 644 " ideal model delta sinusoidal sigma weight residual -35.00 34.01 -69.01 1 8.00e+00 1.56e-02 9.63e+01 dihedral pdb=" O4' U 13119 " pdb=" C1' U 13119 " pdb=" N1 U 13119 " pdb=" C2 U 13119 " ideal model delta sinusoidal sigma weight residual -160.00 19.84 -179.84 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 11300 " pdb=" C1' U 11300 " pdb=" N1 U 11300 " pdb=" C2 U 11300 " ideal model delta sinusoidal sigma weight residual 200.00 29.75 170.25 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 69335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 19846 0.049 - 0.098: 1955 0.098 - 0.146: 537 0.146 - 0.195: 28 0.195 - 0.244: 7 Chirality restraints: 22373 Sorted by residual: chirality pdb=" C3' A 1 359 " pdb=" C4' A 1 359 " pdb=" O3' A 1 359 " pdb=" C2' A 1 359 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' U 11159 " pdb=" C4' U 11159 " pdb=" O3' U 11159 " pdb=" C2' U 11159 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO a 67 " pdb=" N PRO a 67 " pdb=" C PRO a 67 " pdb=" CB PRO a 67 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 22370 not shown) Planarity restraints: 14201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 23 " -0.031 2.00e-02 2.50e+03 2.11e-02 8.92e+00 pdb=" CG TYR K 23 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR K 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR K 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR K 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR K 23 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR K 23 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 23 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 133 " 0.001 2.00e-02 2.50e+03 1.83e-02 7.53e+00 pdb=" N1 U 2 133 " -0.013 2.00e-02 2.50e+03 pdb=" C2 U 2 133 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U 2 133 " 0.019 2.00e-02 2.50e+03 pdb=" N3 U 2 133 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U 2 133 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U 2 133 " -0.012 2.00e-02 2.50e+03 pdb=" C5 U 2 133 " 0.041 2.00e-02 2.50e+03 pdb=" C6 U 2 133 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA m 286 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO m 287 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO m 287 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO m 287 " 0.031 5.00e-02 4.00e+02 ... (remaining 14198 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 4662 2.67 - 3.23: 104911 3.23 - 3.79: 216488 3.79 - 4.34: 285944 4.34 - 4.90: 403241 Nonbonded interactions: 1015246 Sorted by model distance: nonbonded pdb=" O2' A 13367 " pdb=" OP1 A 13368 " model vdw 2.118 2.440 nonbonded pdb=" O2' A 11012 " pdb=" O4' U 11013 " model vdw 2.171 2.440 nonbonded pdb=" O2' A 6 58 " pdb=" OE1 GLN K 56 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR E 177 " pdb=" OD2 ASP M 107 " model vdw 2.196 2.440 nonbonded pdb=" O2' G 11481 " pdb=" O6 G 12443 " model vdw 2.197 2.440 ... (remaining 1015241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 32.350 Check model and map are aligned: 1.300 Set scattering table: 0.790 Process input model: 346.550 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.300 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 394.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.002 0.056 123701 Z= 0.134 Angle : 0.468 11.246 178923 Z= 0.251 Chirality : 0.033 0.244 22373 Planarity : 0.003 0.057 14201 Dihedral : 15.690 179.840 51783 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.95 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 9072 helix: 1.39 (0.09), residues: 3669 sheet: 0.00 (0.14), residues: 1375 loop : -0.11 (0.10), residues: 4028 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 434 time to evaluate : 8.820 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 outliers start: 16 outliers final: 3 residues processed: 445 average time/residue: 1.0525 time to fit residues: 827.0194 Evaluate side-chains 401 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 7.490 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.9259 time to fit residues: 14.0356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 963 optimal weight: 20.0000 chunk 864 optimal weight: 20.0000 chunk 479 optimal weight: 40.0000 chunk 295 optimal weight: 7.9990 chunk 583 optimal weight: 9.9990 chunk 462 optimal weight: 10.0000 chunk 894 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 543 optimal weight: 8.9990 chunk 665 optimal weight: 9.9990 chunk 1036 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 531 ASN D 533 ASN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN N 15 GLN O 43 ASN O 47 HIS P 25 HIS ** i 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 382 HIS m 600 ASN ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS r 72 ASN z 92 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.147 123701 Z= 0.811 Angle : 0.883 13.428 178923 Z= 0.437 Chirality : 0.054 0.337 22373 Planarity : 0.007 0.097 14201 Dihedral : 15.296 179.394 38284 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.09), residues: 9072 helix: 1.30 (0.09), residues: 3701 sheet: -0.28 (0.14), residues: 1355 loop : -0.35 (0.10), residues: 4016 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 389 time to evaluate : 7.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 92 residues processed: 517 average time/residue: 0.9944 time to fit residues: 913.8239 Evaluate side-chains 458 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 366 time to evaluate : 7.542 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.8951 time to fit residues: 159.8834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 575 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 862 optimal weight: 2.9990 chunk 705 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 1038 optimal weight: 50.0000 chunk 1121 optimal weight: 50.0000 chunk 924 optimal weight: 0.8980 chunk 1029 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 832 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 277 GLN B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS P 116 HIS ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 411 GLN n 580 ASN r 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 123701 Z= 0.189 Angle : 0.546 13.057 178923 Z= 0.279 Chirality : 0.037 0.287 22373 Planarity : 0.004 0.059 14201 Dihedral : 14.917 179.256 38284 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.09), residues: 9072 helix: 1.76 (0.09), residues: 3701 sheet: -0.19 (0.14), residues: 1380 loop : -0.19 (0.10), residues: 3991 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 423 time to evaluate : 7.647 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 outliers start: 73 outliers final: 22 residues processed: 484 average time/residue: 0.9894 time to fit residues: 848.5201 Evaluate side-chains 412 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 7.629 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.7761 time to fit residues: 40.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1025 optimal weight: 50.0000 chunk 780 optimal weight: 10.0000 chunk 538 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 495 optimal weight: 50.0000 chunk 697 optimal weight: 2.9990 chunk 1041 optimal weight: 50.0000 chunk 1102 optimal weight: 5.9990 chunk 544 optimal weight: 10.0000 chunk 987 optimal weight: 50.0000 chunk 297 optimal weight: 2.9990 overall best weight: 4.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS Q 78 GLN ** i 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 187 HIS o 211 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 123701 Z= 0.426 Angle : 0.638 12.599 178923 Z= 0.323 Chirality : 0.042 0.288 22373 Planarity : 0.005 0.067 14201 Dihedral : 14.894 179.883 38284 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 9072 helix: 1.70 (0.09), residues: 3697 sheet: -0.21 (0.14), residues: 1361 loop : -0.25 (0.10), residues: 4014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 404 time to evaluate : 7.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 59 residues processed: 493 average time/residue: 1.0522 time to fit residues: 922.5403 Evaluate side-chains 441 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 382 time to evaluate : 7.575 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.8503 time to fit residues: 104.6260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 918 optimal weight: 3.9990 chunk 626 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 821 optimal weight: 0.7980 chunk 455 optimal weight: 10.0000 chunk 941 optimal weight: 3.9990 chunk 762 optimal weight: 40.0000 chunk 1 optimal weight: 0.5980 chunk 563 optimal weight: 0.8980 chunk 989 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN M 81 GLN O 47 HIS O 66 ASN i 19 GLN ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 227 GLN o 187 HIS o 211 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 123701 Z= 0.222 Angle : 0.533 12.904 178923 Z= 0.272 Chirality : 0.037 0.295 22373 Planarity : 0.004 0.063 14201 Dihedral : 14.697 179.293 38284 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 9072 helix: 1.89 (0.09), residues: 3706 sheet: -0.13 (0.14), residues: 1366 loop : -0.20 (0.10), residues: 4000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 414 time to evaluate : 7.632 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 outliers start: 65 outliers final: 28 residues processed: 468 average time/residue: 1.0224 time to fit residues: 845.3410 Evaluate side-chains 422 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 394 time to evaluate : 7.477 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.9115 time to fit residues: 55.5581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 371 optimal weight: 30.0000 chunk 993 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 chunk 647 optimal weight: 40.0000 chunk 272 optimal weight: 9.9990 chunk 1103 optimal weight: 1.9990 chunk 916 optimal weight: 8.9990 chunk 511 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 365 optimal weight: 0.9990 chunk 579 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS O 66 ASN P 171 GLN d 46 GLN ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 10 GLN ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 227 GLN o 160 ASN o 187 HIS o 211 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 123701 Z= 0.311 Angle : 0.563 13.557 178923 Z= 0.287 Chirality : 0.038 0.293 22373 Planarity : 0.004 0.066 14201 Dihedral : 14.649 179.938 38284 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 9072 helix: 1.87 (0.09), residues: 3717 sheet: -0.15 (0.14), residues: 1348 loop : -0.22 (0.10), residues: 4007 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 404 time to evaluate : 7.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 34 residues processed: 455 average time/residue: 0.9947 time to fit residues: 805.2835 Evaluate side-chains 416 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 382 time to evaluate : 7.538 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.8736 time to fit residues: 64.3575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1064 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 628 optimal weight: 0.9980 chunk 806 optimal weight: 50.0000 chunk 624 optimal weight: 10.0000 chunk 929 optimal weight: 1.9990 chunk 616 optimal weight: 9.9990 chunk 1099 optimal weight: 7.9990 chunk 688 optimal weight: 5.9990 chunk 670 optimal weight: 50.0000 chunk 507 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 352 ASN ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 227 GLN n 580 ASN o 187 HIS o 211 HIS r 60 GLN t 63 GLN w 765 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 123701 Z= 0.460 Angle : 0.657 13.693 178923 Z= 0.333 Chirality : 0.043 0.290 22373 Planarity : 0.005 0.067 14201 Dihedral : 14.766 179.845 38284 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 9072 helix: 1.67 (0.09), residues: 3716 sheet: -0.25 (0.14), residues: 1343 loop : -0.30 (0.10), residues: 4013 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 391 time to evaluate : 7.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 25 residues processed: 444 average time/residue: 0.9923 time to fit residues: 780.8282 Evaluate side-chains 402 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 377 time to evaluate : 6.796 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.8216 time to fit residues: 46.1380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 680 optimal weight: 7.9990 chunk 439 optimal weight: 6.9990 chunk 656 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 213 optimal weight: 20.0000 chunk 699 optimal weight: 1.9990 chunk 749 optimal weight: 40.0000 chunk 543 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 864 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 GLN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** e 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 227 GLN o 187 HIS o 211 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 123701 Z= 0.384 Angle : 0.609 13.985 178923 Z= 0.310 Chirality : 0.040 0.297 22373 Planarity : 0.004 0.066 14201 Dihedral : 14.705 179.975 38284 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.56 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 9072 helix: 1.73 (0.09), residues: 3709 sheet: -0.27 (0.14), residues: 1359 loop : -0.28 (0.10), residues: 4004 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 391 time to evaluate : 7.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 33 residues processed: 432 average time/residue: 1.0420 time to fit residues: 799.5788 Evaluate side-chains 415 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 382 time to evaluate : 7.583 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.8468 time to fit residues: 62.3766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1000 optimal weight: 0.9980 chunk 1053 optimal weight: 0.5980 chunk 961 optimal weight: 0.4980 chunk 1024 optimal weight: 10.0000 chunk 616 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 804 optimal weight: 50.0000 chunk 314 optimal weight: 0.8980 chunk 926 optimal weight: 0.9990 chunk 969 optimal weight: 8.9990 chunk 1021 optimal weight: 30.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN F 100 ASN f 4 GLN n 190 GLN o 211 HIS t 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 123701 Z= 0.136 Angle : 0.511 14.478 178923 Z= 0.261 Chirality : 0.035 0.305 22373 Planarity : 0.003 0.060 14201 Dihedral : 14.462 179.702 38284 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 9072 helix: 2.01 (0.09), residues: 3716 sheet: -0.07 (0.14), residues: 1346 loop : -0.15 (0.10), residues: 4010 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 418 time to evaluate : 7.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 430 average time/residue: 1.0380 time to fit residues: 792.4853 Evaluate side-chains 391 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 389 time to evaluate : 7.534 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1505 time to fit residues: 12.6725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 672 optimal weight: 0.2980 chunk 1083 optimal weight: 0.0370 chunk 661 optimal weight: 8.9990 chunk 514 optimal weight: 3.9990 chunk 753 optimal weight: 50.0000 chunk 1136 optimal weight: 7.9990 chunk 1046 optimal weight: 8.9990 chunk 905 optimal weight: 6.9990 chunk 93 optimal weight: 50.0000 chunk 699 optimal weight: 0.9990 chunk 555 optimal weight: 0.4980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN o 160 ASN o 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.106 123701 Z= 0.159 Angle : 0.501 14.512 178923 Z= 0.256 Chirality : 0.035 0.306 22373 Planarity : 0.004 0.062 14201 Dihedral : 14.314 178.985 38284 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 9072 helix: 2.04 (0.09), residues: 3746 sheet: -0.02 (0.14), residues: 1346 loop : -0.10 (0.10), residues: 3980 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18144 Ramachandran restraints generated. 9072 Oldfield, 0 Emsley, 9072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 401 time to evaluate : 7.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 409 average time/residue: 1.0284 time to fit residues: 745.1950 Evaluate side-chains 397 residues out of total 8041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 388 time to evaluate : 7.634 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.8688 time to fit residues: 23.5397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 718 optimal weight: 5.9990 chunk 964 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 834 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 906 optimal weight: 20.0000 chunk 379 optimal weight: 2.9990 chunk 930 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 166 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 593 GLN n 169 HIS n 227 GLN n 580 ASN o 160 ASN o 211 HIS r 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.112368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.105250 restraints weight = 326911.207| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 0.40 r_work: 0.3663 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3549 rms_B_bonded: 2.72 restraints_weight: 0.1250 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 123701 Z= 0.293 Angle : 0.557 14.311 178923 Z= 0.284 Chirality : 0.038 0.303 22373 Planarity : 0.004 0.064 14201 Dihedral : 14.320 178.929 38284 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.87 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 9072 helix: 1.99 (0.09), residues: 3719 sheet: -0.06 (0.14), residues: 1359 loop : -0.11 (0.10), residues: 3994 =============================================================================== Job complete usr+sys time: 18508.94 seconds wall clock time: 330 minutes 23.78 seconds (19823.78 seconds total)