Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 20:41:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esq_24411/04_2023/8esq_24411.pdb" } resolution = 2.8 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= 0.000 sd= 0.011 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 2461 5.49 5 S 219 5.16 5 C 72662 2.51 5 N 24006 2.21 5 O 31060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "Q PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "V GLU 110": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 40": "OE1" <-> "OE2" Residue "Y GLU 82": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "c GLU 69": "OE1" <-> "OE2" Residue "d PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 63": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "h GLU 14": "OE1" <-> "OE2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 86": "OE1" <-> "OE2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "l GLU 7": "OE1" <-> "OE2" Residue "l GLU 14": "OE1" <-> "OE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "l GLU 171": "OE1" <-> "OE2" Residue "m GLU 190": "OE1" <-> "OE2" Residue "m GLU 332": "OE1" <-> "OE2" Residue "o GLU 152": "OE1" <-> "OE2" Residue "o GLU 183": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "t GLU 34": "OE1" <-> "OE2" Residue "t GLU 243": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 130409 Number of models: 1 Model: "" Number of chains: 59 Chain: "7" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1218 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1066 Unresolved non-hydrogen dihedrals: 702 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 460 Chain: "1" Number of atoms: 47746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2230, 47746 Classifications: {'RNA': 2230} Modifications used: {'rna2p_pur': 231, 'rna2p_pyr': 145, 'rna3p_pur': 1024, 'rna3p_pyr': 830} Link IDs: {'rna2p': 375, 'rna3p': 1854} Chain breaks: 38 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': 11, 'rna3p_pur': 62, 'rna3p_pyr': 62} Link IDs: {'rna2p': 25, 'rna3p': 124} Chain breaks: 2 Chain: "3" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1336 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "6" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1717 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 15, 'rna3p_pur': 27, 'rna3p_pyr': 25} Link IDs: {'rna2p': 29, 'rna3p': 51} Chain breaks: 3 Chain: "8" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 291 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1686 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 199} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2687 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} 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: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3396 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 2 Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1283 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "F" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1925 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "G" Number of atoms: 1615 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1607 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 206, 1607 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 1 bond proxies already assigned to first conformer: 1620 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: 3725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3717 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 14, 'TRANS': 445} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 460, 3717 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 14, 'TRANS': 445} Chain breaks: 6 bond proxies already assigned to first conformer: 3765 Chain: "J" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1973 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 236} 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: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 949 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} 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: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "a" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 634 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "b" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 1999 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1278 Unresolved non-hydrogen angles: 1632 Unresolved non-hydrogen dihedrals: 1045 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 8, 'TYR:plan': 15, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 29, 'PHE:plan': 15, 'GLU:plan': 19, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 664 Chain: "c" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 720 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "e" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} 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: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 861 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1418 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "m" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4536 Classifications: {'peptide': 572} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 528} Chain breaks: 6 Chain: "n" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3526 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 411} 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: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1431 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 738 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 9, 'ASP:plan': 22, 'PHE:plan': 10, 'GLU:plan': 9, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 452 Chain: "q" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 1684 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 326} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1070 Unresolved non-hydrogen angles: 1366 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 18, 'GLU:plan': 19, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 592 Chain: "r" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1357 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Chain: "s" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} 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: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} 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: 4067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 504, 4058 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 481} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 504, 4058 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 481} Chain breaks: 4 bond proxies already assigned to first conformer: 4120 Chain: "x" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 383 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 1 Chain: "y" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 269 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 5, 'TRANS': 28} Chain breaks: 1 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 A02D9 SG CYS j 19 129.834 140.028 170.578 1.00 5.88 S ATOM A02E1 SG CYS j 22 132.328 140.875 167.692 1.00 7.45 S ATOM A02GP SG CYS j 34 130.983 137.339 168.222 1.00 0.00 S ATOM A02H6 SG CYS j 37 133.374 138.815 170.710 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALEU I 666 " occ=0.40 ... (14 atoms not shown) pdb=" CD2BLEU I 666 " occ=0.60 residue: pdb=" N AGLU w 243 " occ=0.97 ... (16 atoms not shown) pdb=" OE2BGLU w 243 " occ=0.03 Time building chain proxies: 52.34, per 1000 atoms: 0.40 Number of scatterers: 130409 At special positions: 0 Unit cell: (245.92, 208.82, 320.12, 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 219 16.00 P 2461 15.00 O 31060 8.00 N 24006 7.00 C 72662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 51.29 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " 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 " Number of angles added : 6 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19442 Finding SS restraints... Secondary structure from input PDB file: 389 helices and 98 sheets defined 45.4% alpha, 14.9% beta 787 base pairs and 1399 stacking pairs defined. Time for finding SS restraints: 37.00 Creating SS restraints... Processing helix chain '7' and resid 356 through 369 Processing helix chain '7' and resid 379 through 394 removed outlier: 3.670A pdb=" N ASP 7 394 " --> pdb=" O LEU 7 390 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 418 removed outlier: 3.956A pdb=" N LEU 7 400 " --> pdb=" O GLU 7 396 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE 7 401 " --> pdb=" O SER 7 397 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 430 Processing helix chain '7' and resid 430 through 455 Processing helix chain '7' and resid 458 through 463 Processing helix chain '7' and resid 463 through 478 Processing helix chain '7' and resid 483 through 502 Processing helix chain '7' and resid 507 through 517 Processing helix chain '7' and resid 517 through 522 Processing helix chain '7' and resid 549 through 571 removed outlier: 4.401A pdb=" N THR 7 571 " --> pdb=" O VAL 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 591 Proline residue: 7 581 - end of helix Processing helix chain '7' and resid 600 through 623 Processing helix chain '7' and resid 629 through 640 removed outlier: 3.927A pdb=" N VAL 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 12 Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 72 through 77 removed outlier: 4.738A pdb=" N TRP 3 77 " --> pdb=" O PRO 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 128 Processing helix chain '3' and resid 137 through 156 removed outlier: 4.016A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 162 Processing helix chain '8' and resid 6 through 20 removed outlier: 4.019A pdb=" N ASN 8 20 " --> pdb=" O ALA 8 16 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 30 removed outlier: 3.580A pdb=" N ARG 8 28 " --> pdb=" O PRO 8 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 84 through 94 removed outlier: 4.099A pdb=" N GLU A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'B' and resid 13 through 17 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 154 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.645A pdb=" N THR B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.841A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.570A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (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 265 removed outlier: 4.619A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) 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 90 through 94 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 113 through 125 Proline residue: D 121 - end of helix removed outlier: 3.655A 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 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 200 through 211 removed outlier: 3.597A pdb=" N ASP D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.583A pdb=" N GLY D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 279 through 290 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: 3.824A pdb=" N HIS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 455 removed outlier: 4.017A 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 120 through 125 Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 150 through 171 removed outlier: 4.101A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.666A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 16 through 35 removed outlier: 3.545A pdb=" N GLN F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 80 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.023A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 198 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.345A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 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 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.669A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.941A pdb=" N LEU G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 3.550A 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 239 through 257 removed outlier: 3.946A pdb=" N ALA G 244 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 3.937A 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: 4.055A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.736A pdb=" N GLY H 117 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'I' and resid 214 through 234 Processing helix chain 'I' and resid 235 through 237 No H-bonds generated for 'chain 'I' and resid 235 through 237' Processing helix chain 'I' and resid 238 through 250 removed outlier: 4.095A pdb=" N ILE I 242 " --> pdb=" O ASN I 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG I 243 " --> pdb=" O LEU I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 272 Processing helix chain 'I' and resid 293 through 321 removed outlier: 3.511A pdb=" N HIS I 306 " --> pdb=" O THR I 302 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 347 Processing helix chain 'I' and resid 352 through 365 removed outlier: 3.511A pdb=" N GLN I 363 " --> pdb=" O LEU I 359 " (cutoff:3.500A) 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 421 removed outlier: 3.912A pdb=" N TYR I 416 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I 417 " --> pdb=" O PRO I 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE I 419 " --> pdb=" O VAL I 415 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU I 420 " --> pdb=" O TYR I 416 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 412 through 421' Processing helix chain 'I' and resid 422 through 427 Processing helix chain 'I' and resid 453 through 504 removed outlier: 3.815A 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 520 through 522 No H-bonds generated for 'chain 'I' and resid 520 through 522' Processing helix chain 'I' and resid 523 through 536 removed outlier: 3.573A pdb=" N GLY I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP I 529 " --> pdb=" O GLU I 525 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL I 533 " --> pdb=" O ASP I 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU I 534 " --> pdb=" O LEU I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 570 Processing helix chain 'I' and resid 583 through 600 removed outlier: 3.653A pdb=" N ILE I 594 " --> pdb=" O LEU I 590 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE I 595 " --> pdb=" O TYR I 591 " (cutoff:3.500A) Proline residue: I 596 - end of helix Processing helix chain 'I' and resid 629 through 643 Processing helix chain 'I' and resid 650 through 663 removed outlier: 3.919A pdb=" N SER I 654 " --> pdb=" O SER I 650 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG I 658 " --> pdb=" O SER I 654 " (cutoff:3.500A) Processing helix chain 'I' and resid 667 through 680 removed outlier: 3.598A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 728 removed outlier: 4.221A pdb=" N ASN I 728 " --> pdb=" O PHE I 724 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 744 removed outlier: 3.937A 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 removed outlier: 3.667A pdb=" N ASN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 159 removed outlier: 3.553A pdb=" N LEU J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 211 removed outlier: 3.802A pdb=" N GLU J 206 " --> pdb=" O LYS J 202 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS J 209 " --> pdb=" O ARG J 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 95 through 105 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.668A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.778A 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 154 through 160 removed outlier: 3.684A pdb=" N PHE K 158 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 removed outlier: 3.512A pdb=" N LYS K 226 " --> pdb=" O GLN K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 235 Processing helix chain 'K' and resid 256 through 265 removed outlier: 3.894A pdb=" N ALA K 262 " --> pdb=" O LYS K 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 93 removed outlier: 4.407A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 104 removed outlier: 3.513A pdb=" N GLN M 104 " --> pdb=" O LYS M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 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 Proline residue: N 154 - end of helix removed outlier: 3.608A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 16 through 30 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 101 Processing helix chain 'O' and resid 110 through 115 removed outlier: 3.967A 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 146 Processing helix chain 'O' and resid 150 through 184 removed outlier: 4.123A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 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: 3.511A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.528A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 168 through 182 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 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 48 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.617A pdb=" N ARG R 100 " --> pdb=" O MET R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.926A pdb=" N GLY R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 145 removed outlier: 3.631A pdb=" N LEU R 138 " --> pdb=" O HIS R 134 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) 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 143 Processing helix chain 'U' and resid 16 through 23 Processing helix chain 'U' and resid 26 through 38 Processing helix chain 'U' and resid 39 through 43 Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 70 through 85 removed outlier: 3.662A pdb=" N LEU U 74 " --> pdb=" O SER U 70 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE U 81 " --> pdb=" O LEU U 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU U 82 " --> pdb=" O THR U 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 134 Processing helix chain 'W' and resid 19 through 36 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.899A 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: 3.592A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) removed outlier: 3.694A 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 162 through 169 removed outlier: 4.243A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 205 removed outlier: 3.538A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 8 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 79 removed outlier: 3.598A pdb=" N ASN X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) 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: 3.924A 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 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' 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 76 through 82 removed outlier: 5.592A pdb=" N TRP a 79 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU a 82 " --> pdb=" O TRP a 79 " (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 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.997A 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 Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.698A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 280 Proline residue: b 277 - end of helix Processing helix chain 'b' and resid 306 through 313 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 379 through 384 Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.739A pdb=" N LEU b 454 " --> pdb=" O GLU b 450 " (cutoff:3.500A) Processing helix chain 'c' and resid 23 through 35 Processing helix chain 'c' and resid 40 through 51 Processing helix chain 'c' and resid 63 through 77 Processing helix chain 'c' and resid 87 through 96 Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.522A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 46 removed outlier: 4.162A pdb=" N PHE f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.660A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 removed outlier: 3.588A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 108 Processing helix chain 'h' and resid 4 through 10 Processing helix chain 'h' and resid 12 through 37 Processing helix chain 'h' and resid 39 through 73 removed outlier: 4.135A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.695A 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 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.595A 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 99 Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 64 through 75 removed outlier: 4.479A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 removed outlier: 3.687A pdb=" N SER k 60 " --> pdb=" O LYS k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 21 removed outlier: 3.778A pdb=" N GLU l 14 " --> pdb=" O LYS l 10 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 29 Processing helix chain 'l' and resid 48 through 58 removed outlier: 3.988A pdb=" N SER l 57 " --> pdb=" O LYS l 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL l 58 " --> pdb=" O MET l 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 92 Processing helix chain 'l' and resid 100 through 109 removed outlier: 4.330A 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 146 through 156 Processing helix chain 'm' and resid 176 through 188 Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 260 Processing helix chain 'm' and resid 328 through 343 removed outlier: 3.841A 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 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 74 removed outlier: 4.171A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 removed outlier: 4.266A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS n 80 " --> pdb=" O PRO n 76 " (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: 3.531A 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 241 Processing helix chain 'n' and resid 250 through 256 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 365 through 376 removed outlier: 4.104A pdb=" N PHE n 371 " --> pdb=" O PHE n 367 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE n 376 " --> pdb=" O VAL n 372 " (cutoff:3.500A) Processing helix chain 'n' and resid 384 through 387 Processing helix chain 'n' and resid 420 through 431 removed outlier: 3.793A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) Processing helix chain 'n' and resid 550 through 560 removed outlier: 4.219A pdb=" N GLU n 556 " --> pdb=" O LYS n 552 " (cutoff:3.500A) Processing helix chain 'n' and resid 568 through 571 Processing helix chain 'n' and resid 572 through 599 removed outlier: 4.141A pdb=" N ASN n 578 " --> pdb=" O SER n 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN n 592 " --> pdb=" O ASN n 588 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 129 removed outlier: 4.203A pdb=" N GLN o 127 " --> pdb=" O MET o 123 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY o 129 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 Processing helix chain 'o' and resid 187 through 192 removed outlier: 4.185A pdb=" N PHE o 191 " --> pdb=" O GLU o 188 " (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: 3.585A pdb=" N LYS o 234 " --> pdb=" O LYS o 230 " (cutoff:3.500A) Processing helix chain 'q' and resid 190 through 204 Processing helix chain 'q' and resid 222 through 234 Processing helix chain 'q' and resid 236 through 247 Processing helix chain 'q' and resid 248 through 261 removed outlier: 3.770A pdb=" N GLU q 260 " --> pdb=" O PHE q 256 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET q 261 " --> pdb=" O GLU q 257 " (cutoff:3.500A) Processing helix chain 'q' and resid 275 through 286 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 Processing helix chain 'q' and resid 401 through 406 removed outlier: 3.512A pdb=" N VAL q 406 " --> pdb=" O PHE q 402 " (cutoff:3.500A) Processing helix chain 'q' and resid 421 through 425 removed outlier: 3.756A pdb=" N ILE q 425 " --> pdb=" O THR q 422 " (cutoff:3.500A) Processing helix chain 'q' and resid 429 through 435 removed outlier: 4.250A pdb=" N THR q 433 " --> pdb=" O GLN q 429 " (cutoff:3.500A) Processing helix chain 'q' and resid 436 through 458 Processing helix chain 'q' and resid 476 through 491 removed outlier: 4.100A pdb=" N ALA q 482 " --> pdb=" O ASP q 478 " (cutoff:3.500A) removed outlier: 4.138A 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 14 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.501A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 Processing helix chain 'r' and resid 205 through 211 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 32 Processing helix chain 't' and resid 25 through 47 Processing helix chain 't' and resid 53 through 76 removed outlier: 3.736A 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: 4.015A 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 207 Processing helix chain 't' and resid 219 through 225 Processing helix chain 't' and resid 240 through 249 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 67 through 71 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.622A pdb=" N LEU u 91 " --> pdb=" O ILE u 87 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR u 109 " --> pdb=" O GLU u 105 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 removed outlier: 3.990A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 120 through 126 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.847A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 194 through 207 Processing helix chain 'w' and resid 15 through 24 Processing helix chain 'w' and resid 27 through 41 removed outlier: 3.908A pdb=" N PHE w 31 " --> pdb=" O SER w 27 " (cutoff:3.500A) Processing helix chain 'w' and resid 57 through 67 Processing helix chain 'w' and resid 96 through 108 Processing helix chain 'w' and resid 126 through 148 removed outlier: 3.967A pdb=" N LEU w 144 " --> pdb=" O MET w 140 " (cutoff:3.500A) Processing helix chain 'w' and resid 163 through 175 removed outlier: 4.389A pdb=" N ASN w 167 " --> pdb=" O ARG w 163 " (cutoff:3.500A) Processing helix chain 'w' and resid 208 through 213 Processing helix chain 'w' and resid 213 through 218 Processing helix chain 'w' and resid 227 through 234 removed outlier: 3.826A pdb=" N LYS w 231 " --> pdb=" O ASN w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 264 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 292 Processing helix chain 'w' and resid 296 through 305 Processing helix chain 'w' and resid 310 through 329 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 635 Processing helix chain 'w' and resid 639 through 647 Processing helix chain 'w' and resid 660 through 670 removed outlier: 4.293A 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 718 removed outlier: 4.498A pdb=" N ALA w 703 " --> pdb=" O LYS w 699 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN w 704 " --> pdb=" O VAL w 700 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS w 707 " --> pdb=" O ALA w 703 " (cutoff:3.500A) Processing helix chain 'w' and resid 785 through 796 removed outlier: 4.089A pdb=" N ASP w 789 " --> pdb=" O ARG w 785 " (cutoff:3.500A) Processing helix chain 'x' and resid 6 through 33 Processing helix chain 'y' and resid 12 through 16 removed outlier: 3.538A 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: 4.153A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU y 41 " --> pdb=" O VAL y 37 " (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 177 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 Processing helix chain 'z' and resid 101 through 117 removed outlier: 3.719A pdb=" N ASN z 107 " --> pdb=" O LYS z 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 109 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.979A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 230 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS A 244 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 232 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.979A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 221 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLU A 204 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 202 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 200 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 149 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.877A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.176A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.176A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 84 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 23 removed outlier: 4.578A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.567A pdb=" N GLU C 65 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB3, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.378A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.593A pdb=" N LEU D 364 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR D 393 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS D 338 " --> pdb=" O TRP D 407 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 409 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 340 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE D 408 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE D 440 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN D 410 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY D 314 " --> pdb=" O MET D 439 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU D 441 " --> pdb=" O GLY D 314 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL D 316 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN D 313 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.926A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 71 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'F' and resid 212 through 213 removed outlier: 4.004A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AB9, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AC1, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AC3, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.022A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 130 through 134 removed outlier: 5.966A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.648A pdb=" N VAL H 109 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 198 through 205 removed outlier: 5.622A pdb=" N SER K 198 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR K 59 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N MET K 200 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU K 57 " --> pdb=" O MET K 200 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS K 202 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU K 55 " --> pdb=" O LYS K 202 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY K 204 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA K 237 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 5.271A 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=AC7, first strand: chain 'K' and resid 72 through 75 removed outlier: 3.685A pdb=" N PHE K 191 " --> pdb=" O TYR K 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.564A pdb=" N ALA K 87 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE K 115 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU K 89 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 22 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD2, first strand: chain 'L' and resid 123 through 126 removed outlier: 4.682A pdb=" N LYS h 117 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.629A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE M 61 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU M 15 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR M 59 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.510A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.081A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AD7, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.639A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.302A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AE2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE3, first strand: chain 'S' and resid 55 through 62 removed outlier: 5.104A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 87 through 95 removed outlier: 6.482A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 51 through 53 removed outlier: 4.730A pdb=" N LEU U 103 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL U 100 " --> pdb=" O THR U 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AE7, first strand: chain 'V' and resid 24 through 27 removed outlier: 6.086A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 87 through 88 removed outlier: 5.668A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AF1, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.424A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS X 108 " --> pdb=" O LYS X 124 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF3, first strand: chain 'Y' and resid 93 through 98 removed outlier: 6.456A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR Y 56 " --> pdb=" O ILE Y 105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE Y 105 " --> pdb=" O THR Y 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.474A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 75 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS Z 40 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS Z 22 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS Z 21 " --> pdb=" O ILE Z 13 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR Z 85 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU Z 12 " --> pdb=" O THR Z 83 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR Z 83 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.426A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.225A pdb=" N ILE a 101 " --> pdb=" O GLN a 125 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR a 126 " --> pdb=" O GLU a 145 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 206 through 211 removed outlier: 6.952A pdb=" N THR b 170 " --> pdb=" O ALA b 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 254 through 256 removed outlier: 5.735A pdb=" N LEU b 288 " --> pdb=" O THR b 321 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 37 through 39 removed outlier: 6.246A pdb=" N ILE c 56 " --> pdb=" O HIS c 82 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR c 84 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE c 58 " --> pdb=" O TYR c 84 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 54 through 56 removed outlier: 6.399A pdb=" N ARG d 55 " --> pdb=" O VAL d 96 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA d 98 " --> pdb=" O ARG d 55 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR d 14 " --> pdb=" O VAL d 111 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AG3, first strand: chain 'f' and resid 10 through 19 removed outlier: 5.841A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA f 81 " --> pdb=" O HIS f 76 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG5, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG6, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.735A pdb=" N ARG k 3 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N VAL k 47 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'l' and resid 37 through 40 removed outlier: 6.357A pdb=" N VAL l 44 " --> pdb=" O PHE l 70 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 65 through 66 removed outlier: 4.253A pdb=" N SER l 65 " --> pdb=" O VAL q 394 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL q 394 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE q 367 " --> pdb=" O ILE q 393 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N CYS q 395 " --> pdb=" O ILE q 367 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA q 369 " --> pdb=" O CYS q 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 342 " --> pdb=" O ARG q 412 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU q 414 " --> pdb=" O ARG q 342 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU q 344 " --> pdb=" O LEU q 414 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP q 416 " --> pdb=" O LEU q 344 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS q 540 " --> pdb=" O VAL q 497 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 65 through 66 removed outlier: 4.253A pdb=" N SER l 65 " --> pdb=" O VAL q 394 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL q 394 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE q 367 " --> pdb=" O ILE q 393 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N CYS q 395 " --> pdb=" O ILE q 367 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA q 369 " --> pdb=" O CYS q 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 342 " --> pdb=" O ARG q 412 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU q 414 " --> pdb=" O ARG q 342 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU q 344 " --> pdb=" O LEU q 414 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP q 416 " --> pdb=" O LEU q 344 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'l' and resid 113 through 114 removed outlier: 3.576A pdb=" N ALA l 163 " --> pdb=" O VAL l 113 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE l 143 " --> pdb=" O GLN l 166 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP l 168 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU l 141 " --> pdb=" O ASP l 168 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY l 142 " --> pdb=" O ILE l 133 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE l 97 " --> pdb=" O TYR l 134 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP l 98 " --> pdb=" O GLY l 119 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 118 through 119 removed outlier: 3.535A pdb=" N GLY m 118 " --> pdb=" O VAL m 165 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE m 164 " --> pdb=" O VAL m 173 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 345 through 348 Processing sheet with id=AH4, first strand: chain 'm' and resid 388 through 391 Processing sheet with id=AH5, first strand: chain 'm' and resid 454 through 457 removed outlier: 3.721A pdb=" N SER m 454 " --> pdb=" O ALA m 469 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 533 through 536 Processing sheet with id=AH7, first strand: chain 'm' and resid 576 through 581 removed outlier: 4.286A pdb=" N TYR m 595 " --> pdb=" O THR m 592 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL m 596 " --> pdb=" O THR m 609 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR m 609 " --> pdb=" O VAL m 596 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE m 598 " --> pdb=" O VAL m 607 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'm' and resid 617 through 622 Processing sheet with id=AH9, first strand: chain 'm' and resid 660 through 665 removed outlier: 5.990A pdb=" N VAL m 681 " --> pdb=" O ILE m 703 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE m 703 " --> pdb=" O VAL m 681 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL m 683 " --> pdb=" O LEU m 701 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'm' and resid 717 through 720 removed outlier: 3.776A pdb=" N SER m 717 " --> pdb=" O ALA m 730 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AI3, first strand: chain 'n' and resid 177 through 182 removed outlier: 5.558A pdb=" N LEU n 177 " --> pdb=" O GLU n 192 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU n 192 " --> pdb=" O LEU n 177 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'n' and resid 379 through 382 removed outlier: 6.300A pdb=" N THR n 357 " --> pdb=" O HIS n 401 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE n 403 " --> pdb=" O THR n 357 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE n 359 " --> pdb=" O ILE n 403 " (cutoff:3.500A) removed outlier: 6.087A 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: 4.820A pdb=" N VAL o 131 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU o 152 " --> pdb=" O VAL o 131 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG o 133 " --> pdb=" O PHE o 150 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE o 150 " --> pdb=" O ARG o 133 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ARG o 135 " --> pdb=" O TYR o 148 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR o 148 " --> pdb=" O ARG o 135 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER o 137 " --> pdb=" O LYS o 146 " (cutoff:3.500A) removed outlier: 4.535A 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: 6.574A pdb=" N ILE p 430 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER p 100 " --> pdb=" O LEU p 428 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU p 428 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN p 427 " --> pdb=" O GLY p 423 " (cutoff:3.500A) removed outlier: 4.701A 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 removed outlier: 6.019A pdb=" N ALA p 126 " --> pdb=" O GLN p 138 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN p 138 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL p 128 " --> pdb=" O LYS p 136 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'p' and resid 146 through 151 removed outlier: 4.098A pdb=" N SER p 148 " --> pdb=" O ALA p 161 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS p 166 " --> pdb=" O SER p 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR p 191 " --> pdb=" O HIS p 169 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL p 171 " --> pdb=" O LEU p 189 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU p 189 " --> pdb=" O VAL p 171 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 200 through 203 removed outlier: 3.991A pdb=" N THR p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'p' and resid 274 through 277 removed outlier: 4.052A pdb=" N ASP p 305 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP p 297 " --> pdb=" O ASN p 303 " (cutoff:3.500A) removed outlier: 5.957A 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 removed outlier: 4.062A pdb=" N CYS p 315 " --> pdb=" O GLY p 328 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS p 333 " --> pdb=" O SER p 329 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'p' and resid 358 through 363 removed outlier: 4.069A pdb=" N THR p 379 " --> pdb=" O SER p 375 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'q' and resid 288 through 292 removed outlier: 6.635A pdb=" N ASN q 289 " --> pdb=" O PHE q 304 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL q 265 " --> pdb=" O VAL q 303 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 510 through 511 Processing sheet with id=AJ6, first strand: chain 'r' and resid 180 through 184 removed outlier: 6.816A pdb=" N VAL r 219 " --> pdb=" O LYS r 200 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA r 256 " --> pdb=" O LYS r 180 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN r 182 " --> pdb=" O ALA r 256 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU r 258 " --> pdb=" O ASN r 182 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR r 184 " --> pdb=" O LEU r 258 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 't' and resid 211 through 212 removed outlier: 4.456A pdb=" N ASN t 119 " --> pdb=" O ARG t 94 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL t 140 " --> pdb=" O GLY t 235 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS t 237 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR t 142 " --> pdb=" O CYS t 237 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 't' and resid 165 through 168 removed outlier: 4.772A pdb=" N PHE t 159 " --> pdb=" O TRP t 209 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AK1, first strand: chain 'w' and resid 87 through 91 removed outlier: 6.817A pdb=" N VAL w 48 " --> pdb=" O ALA w 112 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP w 113 " --> pdb=" O THR w 154 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL w 156 " --> pdb=" O ASP w 113 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL w 115 " --> pdb=" O VAL w 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS w 158 " --> pdb=" O VAL w 115 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS w 117 " --> pdb=" O LYS w 158 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N PHE w 160 " --> pdb=" O HIS w 117 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY w 153 " --> pdb=" O GLY w 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS w 198 " --> pdb=" O VAL w 179 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL w 179 " --> pdb=" O CYS w 198 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY w 200 " --> pdb=" O ASN w 177 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'w' and resid 255 through 257 Processing sheet with id=AK3, first strand: chain 'w' and resid 757 through 760 removed outlier: 6.040A pdb=" N THR w 757 " --> pdb=" O LYS w 780 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL w 782 " --> pdb=" O THR w 757 " (cutoff:3.500A) removed outlier: 6.314A 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 5 removed outlier: 6.051A 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: 6.901A 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 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 removed outlier: 6.372A pdb=" N ALA y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 3786 hydrogen bonds defined for protein. 10866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1920 hydrogen bonds 3116 hydrogen bond angles 0 basepair planarities 787 basepair parallelities 1399 stacking parallelities Total time for adding SS restraints: 140.49 Time building geometry restraints manager: 55.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26785 1.33 - 1.46: 44649 1.46 - 1.58: 61251 1.58 - 1.70: 4877 1.70 - 1.82: 350 Bond restraints: 137912 Sorted by residual: bond pdb=" CA ASP m 156 " pdb=" CB ASP m 156 " ideal model delta sigma weight residual 1.527 1.621 -0.095 1.75e-02 3.27e+03 2.92e+01 bond pdb=" C PHE m 225 " pdb=" N ALA m 226 " ideal model delta sigma weight residual 1.333 1.278 0.055 2.74e-02 1.33e+03 3.96e+00 bond pdb=" C ASP y 90 " pdb=" N PRO y 91 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 2.99e+00 bond pdb=" C GLU n 394 " pdb=" O GLU n 394 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.26e-02 6.30e+03 2.74e+00 bond pdb=" CB LYS n 558 " pdb=" CG LYS n 558 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 137907 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.65: 6867 103.65 - 111.35: 69429 111.35 - 119.04: 51021 119.04 - 126.73: 63324 126.73 - 134.42: 7633 Bond angle restraints: 198274 Sorted by residual: angle pdb=" N ILE n 133 " pdb=" CA ILE n 133 " pdb=" C ILE n 133 " ideal model delta sigma weight residual 113.71 109.03 4.68 9.50e-01 1.11e+00 2.43e+01 angle pdb=" N LYS E 135 " pdb=" CA LYS E 135 " pdb=" C LYS E 135 " ideal model delta sigma weight residual 110.91 116.35 -5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" CB MET w 142 " pdb=" CG MET w 142 " pdb=" SD MET w 142 " ideal model delta sigma weight residual 112.70 126.14 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C4' G 11173 " pdb=" C3' G 11173 " pdb=" O3' G 11173 " ideal model delta sigma weight residual 113.00 106.35 6.65 1.50e+00 4.44e-01 1.96e+01 angle pdb=" C MET R 57 " pdb=" CA MET R 57 " pdb=" CB MET R 57 " ideal model delta sigma weight residual 110.42 119.21 -8.79 1.99e+00 2.53e-01 1.95e+01 ... (remaining 198269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 75197 35.89 - 71.77: 2587 71.77 - 107.66: 225 107.66 - 143.55: 23 143.55 - 179.44: 32 Dihedral angle restraints: 78064 sinusoidal: 48162 harmonic: 29902 Sorted by residual: dihedral pdb=" C5' U 11806 " pdb=" C4' U 11806 " pdb=" C3' U 11806 " pdb=" O3' U 11806 " ideal model delta sinusoidal sigma weight residual 147.00 76.69 70.31 1 8.00e+00 1.56e-02 9.95e+01 dihedral pdb=" C4' U 11806 " pdb=" C3' U 11806 " pdb=" C2' U 11806 " pdb=" C1' U 11806 " ideal model delta sinusoidal sigma weight residual -35.00 34.94 -69.94 1 8.00e+00 1.56e-02 9.86e+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 200.00 23.03 176.97 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 78061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 22977 0.075 - 0.149: 1357 0.149 - 0.224: 77 0.224 - 0.298: 7 0.298 - 0.373: 2 Chirality restraints: 24420 Sorted by residual: chirality pdb=" C3' U 11806 " pdb=" C4' U 11806 " pdb=" O3' U 11806 " pdb=" C2' U 11806 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE n 428 " pdb=" CA ILE n 428 " pdb=" CG1 ILE n 428 " pdb=" CG2 ILE n 428 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' A 13367 " pdb=" C4' A 13367 " pdb=" O3' A 13367 " pdb=" C2' A 13367 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 24417 not shown) Planarity restraints: 16172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 125 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO J 126 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO J 126 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO J 126 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL t 83 " -0.061 5.00e-02 4.00e+02 9.27e-02 1.38e+01 pdb=" N PRO t 84 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO t 84 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO t 84 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR l 125 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO l 126 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO l 126 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO l 126 " 0.044 5.00e-02 4.00e+02 ... (remaining 16169 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 6028 2.69 - 3.24: 123312 3.24 - 3.79: 247852 3.79 - 4.35: 327121 4.35 - 4.90: 460014 Nonbonded interactions: 1164327 Sorted by model distance: nonbonded pdb=" O2' A 1 997 " pdb=" O4' U 1 998 " model vdw 2.136 2.440 nonbonded pdb=" O2' A 11012 " pdb=" O4' U 11013 " model vdw 2.153 2.440 nonbonded pdb=" N GLU Q 21 " pdb=" OE1 GLU Q 21 " model vdw 2.175 2.520 nonbonded pdb=" O2' U 11806 " pdb=" O5' G 11807 " model vdw 2.187 2.440 nonbonded pdb=" N GLU Y 37 " pdb=" OE1 GLU Y 37 " model vdw 2.189 2.520 ... (remaining 1164322 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=0.00 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: 5.250 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: 0.100 Extract box with map and model: 32.740 Check model and map are aligned: 1.560 Set scattering table: 0.860 Process input model: 397.170 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.390 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: 0.030 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 453.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.095 137912 Z= 0.205 Angle : 0.556 13.440 198274 Z= 0.298 Chirality : 0.036 0.373 24420 Planarity : 0.004 0.106 16172 Dihedral : 15.883 179.437 58622 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 0.54 (0.09), residues: 10056 helix: 1.22 (0.08), residues: 4247 sheet: -0.16 (0.13), residues: 1411 loop : -0.22 (0.10), residues: 4398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 716 time to evaluate : 8.081 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: 76 outliers final: 32 residues processed: 770 average time/residue: 1.8230 time to fit residues: 2040.5423 Evaluate side-chains 671 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 639 time to evaluate : 8.059 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 3 average time/residue: 1.2266 time to fit residues: 16.2117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1054 optimal weight: 50.0000 chunk 946 optimal weight: 30.0000 chunk 525 optimal weight: 6.9990 chunk 323 optimal weight: 8.9990 chunk 638 optimal weight: 0.0870 chunk 505 optimal weight: 5.9990 chunk 978 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 595 optimal weight: 7.9990 chunk 728 optimal weight: 0.8980 chunk 1134 optimal weight: 0.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 41 GLN 8 11 GLN B 11 HIS ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 117 HIS l 166 GLN ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 408 HIS ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 580 ASN n 585 ASN ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 127 GLN ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS r 72 ASN u 24 ASN u 101 HIS ** y 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 137912 Z= 0.302 Angle : 0.626 10.913 198274 Z= 0.319 Chirality : 0.041 0.389 24420 Planarity : 0.005 0.082 16172 Dihedral : 15.029 179.714 40585 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 10056 helix: 1.61 (0.08), residues: 4265 sheet: -0.18 (0.13), residues: 1436 loop : -0.25 (0.10), residues: 4355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 688 time to evaluate : 8.209 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 outliers start: 204 outliers final: 83 residues processed: 817 average time/residue: 1.8130 time to fit residues: 2170.5064 Evaluate side-chains 716 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 633 time to evaluate : 7.419 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 58 residues processed: 26 average time/residue: 1.1412 time to fit residues: 58.3215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 630 optimal weight: 5.9990 chunk 352 optimal weight: 0.0040 chunk 943 optimal weight: 0.9980 chunk 772 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 chunk 1136 optimal weight: 0.8980 chunk 1227 optimal weight: 20.0000 chunk 1011 optimal weight: 3.9990 chunk 1126 optimal weight: 3.9990 chunk 387 optimal weight: 4.9990 chunk 911 optimal weight: 50.0000 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN ** K 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** R 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN V 83 GLN i 93 GLN ** k 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 117 HIS l 166 GLN ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 190 GLN ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS r 72 ASN ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 86 ASN ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 137912 Z= 0.217 Angle : 0.565 10.674 198274 Z= 0.290 Chirality : 0.038 0.367 24420 Planarity : 0.004 0.067 16172 Dihedral : 14.891 179.052 40585 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 10056 helix: 1.71 (0.08), residues: 4251 sheet: -0.14 (0.13), residues: 1427 loop : -0.22 (0.10), residues: 4378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 702 time to evaluate : 8.271 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: 210 outliers final: 84 residues processed: 848 average time/residue: 1.8018 time to fit residues: 2253.0905 Evaluate side-chains 718 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 634 time to evaluate : 8.144 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 63 residues processed: 24 average time/residue: 1.1709 time to fit residues: 58.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1122 optimal weight: 4.9990 chunk 854 optimal weight: 3.9990 chunk 589 optimal weight: 4.9990 chunk 125 optimal weight: 50.0000 chunk 542 optimal weight: 8.9990 chunk 762 optimal weight: 2.9990 chunk 1140 optimal weight: 20.0000 chunk 1207 optimal weight: 0.6980 chunk 595 optimal weight: 7.9990 chunk 1080 optimal weight: 50.0000 chunk 325 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN N 192 HIS R 141 HIS V 22 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN l 117 HIS m 352 ASN m 382 HIS ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 569 GLN ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 247 ASN ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN y 86 ASN ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 89 ASN ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 137912 Z= 0.340 Angle : 0.631 14.831 198274 Z= 0.321 Chirality : 0.041 0.405 24420 Planarity : 0.005 0.084 16172 Dihedral : 14.930 179.860 40585 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 0.77 (0.09), residues: 10056 helix: 1.62 (0.08), residues: 4261 sheet: -0.20 (0.13), residues: 1431 loop : -0.28 (0.10), residues: 4364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 680 time to evaluate : 8.414 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 outliers start: 229 outliers final: 110 residues processed: 841 average time/residue: 1.8406 time to fit residues: 2277.0510 Evaluate side-chains 739 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 629 time to evaluate : 8.238 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 87 residues processed: 26 average time/residue: 1.2773 time to fit residues: 65.3117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1005 optimal weight: 9.9990 chunk 685 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 898 optimal weight: 7.9990 chunk 498 optimal weight: 10.0000 chunk 1030 optimal weight: 0.9990 chunk 834 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 616 optimal weight: 0.6980 chunk 1083 optimal weight: 50.0000 chunk 304 optimal weight: 30.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS O 5 GLN ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 117 HIS ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 585 ASN ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS r 72 ASN ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 137912 Z= 0.306 Angle : 0.606 13.330 198274 Z= 0.308 Chirality : 0.040 0.404 24420 Planarity : 0.005 0.080 16172 Dihedral : 14.878 179.336 40585 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 10056 helix: 1.66 (0.08), residues: 4242 sheet: -0.20 (0.13), residues: 1439 loop : -0.29 (0.10), residues: 4375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 668 time to evaluate : 8.198 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: 218 outliers final: 112 residues processed: 827 average time/residue: 1.8190 time to fit residues: 2222.6140 Evaluate side-chains 742 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 630 time to evaluate : 8.156 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 90 residues processed: 25 average time/residue: 1.3267 time to fit residues: 64.1997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 406 optimal weight: 5.9990 chunk 1087 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 1208 optimal weight: 3.9990 chunk 1003 optimal weight: 0.0070 chunk 559 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 399 optimal weight: 10.0000 chunk 634 optimal weight: 1.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS R 58 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 165 HIS ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 585 ASN ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 86 ASN ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 137912 Z= 0.391 Angle : 0.658 13.449 198274 Z= 0.333 Chirality : 0.043 0.426 24420 Planarity : 0.005 0.089 16172 Dihedral : 14.922 179.752 40585 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 10056 helix: 1.59 (0.08), residues: 4241 sheet: -0.24 (0.13), residues: 1445 loop : -0.31 (0.10), residues: 4370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 658 time to evaluate : 8.260 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: 237 outliers final: 130 residues processed: 832 average time/residue: 1.7974 time to fit residues: 2198.9849 Evaluate side-chains 754 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 624 time to evaluate : 8.124 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 103 residues processed: 30 average time/residue: 1.2202 time to fit residues: 71.6879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1165 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 688 optimal weight: 9.9990 chunk 882 optimal weight: 0.9990 chunk 683 optimal weight: 2.9990 chunk 1017 optimal weight: 6.9990 chunk 674 optimal weight: 30.0000 chunk 1203 optimal weight: 5.9990 chunk 753 optimal weight: 5.9990 chunk 733 optimal weight: 6.9990 chunk 555 optimal weight: 6.9990 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 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 165 HIS ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN y 86 ASN y 157 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 137912 Z= 0.296 Angle : 0.606 12.372 198274 Z= 0.309 Chirality : 0.040 0.411 24420 Planarity : 0.005 0.090 16172 Dihedral : 14.825 179.664 40585 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 0.75 (0.09), residues: 10056 helix: 1.62 (0.08), residues: 4258 sheet: -0.22 (0.13), residues: 1435 loop : -0.30 (0.10), residues: 4363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 662 time to evaluate : 8.596 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 outliers start: 212 outliers final: 117 residues processed: 823 average time/residue: 1.7969 time to fit residues: 2173.7725 Evaluate side-chains 738 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 621 time to evaluate : 8.184 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 100 residues processed: 18 average time/residue: 1.3894 time to fit residues: 50.1726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 744 optimal weight: 5.9990 chunk 480 optimal weight: 0.0870 chunk 718 optimal weight: 40.0000 chunk 362 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 765 optimal weight: 20.0000 chunk 820 optimal weight: 10.0000 chunk 595 optimal weight: 3.9990 chunk 112 optimal weight: 30.0000 chunk 946 optimal weight: 7.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 165 HIS ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 382 HIS ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 HIS ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 137912 Z= 0.412 Angle : 0.676 12.109 198274 Z= 0.341 Chirality : 0.043 0.424 24420 Planarity : 0.006 0.171 16172 Dihedral : 14.891 179.946 40585 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 0.66 (0.09), residues: 10056 helix: 1.54 (0.08), residues: 4240 sheet: -0.25 (0.13), residues: 1435 loop : -0.34 (0.10), residues: 4381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 640 time to evaluate : 8.305 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 outliers start: 209 outliers final: 132 residues processed: 803 average time/residue: 1.7988 time to fit residues: 2132.8334 Evaluate side-chains 751 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 619 time to evaluate : 8.184 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 107 residues processed: 26 average time/residue: 1.3670 time to fit residues: 67.6517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1095 optimal weight: 7.9990 chunk 1153 optimal weight: 3.9990 chunk 1052 optimal weight: 50.0000 chunk 1121 optimal weight: 0.9980 chunk 1152 optimal weight: 0.7980 chunk 675 optimal weight: 6.9990 chunk 488 optimal weight: 7.9990 chunk 880 optimal weight: 0.9980 chunk 344 optimal weight: 0.2980 chunk 1013 optimal weight: 0.9990 chunk 1061 optimal weight: 50.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 110 GLN ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN S 61 ASN ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 137912 Z= 0.152 Angle : 0.557 13.831 198274 Z= 0.284 Chirality : 0.036 0.377 24420 Planarity : 0.004 0.079 16172 Dihedral : 14.666 179.249 40585 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: 0.88 (0.09), residues: 10056 helix: 1.74 (0.08), residues: 4247 sheet: -0.15 (0.13), residues: 1425 loop : -0.24 (0.10), residues: 4384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 663 time to evaluate : 12.227 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 outliers start: 160 outliers final: 110 residues processed: 800 average time/residue: 1.7910 time to fit residues: 2118.0396 Evaluate side-chains 739 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 629 time to evaluate : 8.180 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 103 residues processed: 8 average time/residue: 1.2699 time to fit residues: 26.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 1117 optimal weight: 3.9990 chunk 736 optimal weight: 6.9990 chunk 1186 optimal weight: 4.9990 chunk 724 optimal weight: 40.0000 chunk 562 optimal weight: 1.9990 chunk 824 optimal weight: 30.0000 chunk 1244 optimal weight: 30.0000 chunk 1145 optimal weight: 9.9990 chunk 990 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 765 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 137912 Z= 0.310 Angle : 0.618 14.706 198274 Z= 0.313 Chirality : 0.040 0.401 24420 Planarity : 0.005 0.127 16172 Dihedral : 14.662 179.440 40585 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.83 (0.09), residues: 10056 helix: 1.67 (0.08), residues: 4241 sheet: -0.17 (0.13), residues: 1423 loop : -0.24 (0.10), residues: 4392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20112 Ramachandran restraints generated. 10056 Oldfield, 0 Emsley, 10056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 640 time to evaluate : 8.432 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 outliers start: 140 outliers final: 110 residues processed: 762 average time/residue: 1.8301 time to fit residues: 2073.1616 Evaluate side-chains 733 residues out of total 8899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 623 time to evaluate : 8.474 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 105 residues processed: 5 average time/residue: 1.5788 time to fit residues: 22.5648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1249 random chunks: chunk 607 optimal weight: 0.6980 chunk 787 optimal weight: 10.0000 chunk 1055 optimal weight: 30.0000 chunk 303 optimal weight: 0.3980 chunk 913 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 992 optimal weight: 0.9990 chunk 415 optimal weight: 0.9980 chunk 1019 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN S 61 ASN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 4 GLN ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.143449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.132525 restraints weight = 324953.051| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 0.42 r_work: 0.4042 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3879 rms_B_bonded: 4.06 restraints_weight: 0.1250 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 137912 Z= 0.239 Angle : 0.587 16.701 198274 Z= 0.298 Chirality : 0.038 0.386 24420 Planarity : 0.005 0.108 16172 Dihedral : 14.593 179.481 40585 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.84 (0.09), residues: 10056 helix: 1.68 (0.08), residues: 4247 sheet: -0.16 (0.13), residues: 1429 loop : -0.23 (0.10), residues: 4380 =============================================================================== Job complete usr+sys time: 34358.55 seconds wall clock time: 601 minutes 22.95 seconds (36082.95 seconds total)