Starting phenix.real_space_refine on Fri Mar 1 01:26:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msc_23961/03_2024/7msc_23961_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 4842 5.49 5 Mg 445 5.21 5 S 102 5.16 5 C 76301 2.51 5 N 28471 2.21 5 O 42280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 55": "NH1" <-> "NH2" Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "P TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 112": "NH1" <-> "NH2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "x ARG 12": "NH1" <-> "NH2" Residue "x ARG 233": "NH1" <-> "NH2" Residue "x TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 257": "NH1" <-> "NH2" Residue "x ARG 265": "NH1" <-> "NH2" Residue "x ARG 302": "NH1" <-> "NH2" Residue "x ARG 346": "NH1" <-> "NH2" Residue "x ARG 399": "NH1" <-> "NH2" Residue "x ARG 539": "NH1" <-> "NH2" Residue "x ARG 553": "NH1" <-> "NH2" Residue "x ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152447 Number of models: 1 Model: "" Number of chains: 69 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain breaks: 1 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 186 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66958 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 1, 'rna2p_pur': 299, 'rna2p_pyr': 156, 'rna3p': 1, 'rna3p_pur': 1483, 'rna3p_pyr': 1178} Link IDs: {'rna2p': 456, 'rna3p': 2661} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 560 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 93, 'rna3p': 6, 'rna3p_pur': 733, 'rna3p_pyr': 569} Link IDs: {'rna2p': 211, 'rna3p': 1307} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "x" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4279 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 23, 'TRANS': 523} Chain breaks: 1 Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "z" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Unusual residues: {' MG': 301} Classifications: {'undetermined': 301} Link IDs: {None: 300} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Unusual residues: {' MG': 130} Classifications: {'undetermined': 130} Link IDs: {None: 129} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "y" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 116.516 179.669 187.215 1.00 58.86 S ATOM 519 SG CYS 1 18 116.424 183.263 185.400 1.00 59.77 S ATOM 734 SG CYS 1 42 119.972 182.035 185.784 1.00 54.50 S ATOM 755 SG CYS 1 45 117.925 183.431 188.827 1.00 56.35 S ATOM 1789 SG CYS 4 11 184.465 98.943 135.913 1.00 73.02 S ATOM 1812 SG CYS 4 14 185.431 102.133 134.636 1.00 71.55 S ATOM 1922 SG CYS 4 27 186.631 99.645 132.237 1.00 70.10 S ATOM 2132 SG CYS 6 16 113.617 113.684 223.571 1.00 97.07 S ATOM 2291 SG CYS 6 38 117.250 113.533 223.703 1.00 92.50 S ATOM 2312 SG CYS 6 41 115.381 110.680 222.525 1.00 93.59 S ATOM 95004 SG CYS X 5 91.260 201.026 121.821 1.00 53.43 S ATOM 95026 SG CYS X 8 93.148 203.292 124.233 1.00 56.83 S ATOM 95369 SG CYS X 52 91.076 199.924 125.624 1.00 54.02 S ATOM 95388 SG CYS X 55 89.250 202.964 125.026 1.00 57.71 S ATOM A0VWU SG CYS n 24 90.230 56.099 169.763 1.00 63.95 S ATOM A0VXF SG CYS n 27 92.103 57.266 166.522 1.00 64.28 S ATOM A0W0D SG CYS n 40 89.057 59.548 167.994 1.00 62.54 S ATOM A0W12 SG CYS n 43 88.211 56.478 166.265 1.00 63.94 S ATOM A0XZ9 SG CYS r 20 34.764 120.156 107.502 1.00 86.89 S ATOM A0XZX SG CYS r 23 34.598 119.067 103.843 1.00 92.63 S ATOM A0Y7I SG CYS r 57 38.036 119.279 104.950 1.00 74.31 S Time building chain proxies: 58.03, per 1000 atoms: 0.38 Number of scatterers: 152447 At special positions: 0 Unit cell: (240.62, 270.3, 242.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 102 16.00 P 4842 15.00 Mg 445 11.99 O 42280 8.00 N 28471 7.00 C 76301 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.05 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " Number of angles added : 24 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11262 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 183 helices and 79 sheets defined 37.1% alpha, 18.9% beta 1207 base pairs and 2746 stacking pairs defined. Time for finding SS restraints: 75.24 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 3.513A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.872A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG 0 48 " --> pdb=" O LEU 0 44 " (cutoff:3.500A) Processing helix chain '1' and resid 28 through 33 Proline residue: 1 33 - end of helix No H-bonds generated for 'chain '1' and resid 28 through 33' Processing helix chain '2' and resid 11 through 19 removed outlier: 3.579A pdb=" N ALA 2 16 " --> pdb=" O ASN 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 27 removed outlier: 4.158A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 41 removed outlier: 3.944A pdb=" N ILE 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 2 39 " --> pdb=" O SER 2 35 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.565A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 46 removed outlier: 3.914A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.608A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 3 58 " --> pdb=" O ASP 3 54 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR 3 59 " --> pdb=" O THR 3 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 3 63 " --> pdb=" O THR 3 59 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 3.805A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '6' and resid 56 through 65 removed outlier: 4.011A pdb=" N ARG 6 60 " --> pdb=" O GLY 6 56 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS 6 63 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG 6 64 " --> pdb=" O ARG 6 60 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 12 removed outlier: 4.270A pdb=" N ARG 7 6 " --> pdb=" O ALA 7 2 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG 7 11 " --> pdb=" O LYS 7 7 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS 7 12 " --> pdb=" O LYS 7 8 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 15 removed outlier: 4.214A pdb=" N ALA 8 12 " --> pdb=" O TYR 8 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 8 13 " --> pdb=" O ARG 8 9 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS 8 14 " --> pdb=" O ALA 8 10 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 8 through 15' Processing helix chain '8' and resid 22 through 34 removed outlier: 3.800A pdb=" N ALA 8 27 " --> pdb=" O PRO 8 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 8 32 " --> pdb=" O LYS 8 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR 8 33 " --> pdb=" O LEU 8 29 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER 8 34 " --> pdb=" O ALA 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 3.663A pdb=" N VAL 8 88 " --> pdb=" O ALA 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 98 through 107 removed outlier: 4.925A pdb=" N GLU 8 102 " --> pdb=" O ASP 8 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG 8 103 " --> pdb=" O ASP 8 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN 8 105 " --> pdb=" O ILE 8 101 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 129 removed outlier: 4.309A pdb=" N ALA 8 122 " --> pdb=" O PRO 8 118 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS 8 123 " --> pdb=" O ASP 8 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL 8 124 " --> pdb=" O GLN 8 120 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY 8 125 " --> pdb=" O MET 8 121 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG 8 126 " --> pdb=" O ALA 8 122 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE 8 127 " --> pdb=" O LYS 8 123 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 135 removed outlier: 4.762A pdb=" N ARG 8 134 " --> pdb=" O VAL 8 130 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY 8 135 " --> pdb=" O LEU 8 131 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 130 through 135' Processing helix chain '8' and resid 148 through 159 removed outlier: 4.410A pdb=" N ALA 8 152 " --> pdb=" O ASP 8 148 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 3.745A pdb=" N ALA 8 186 " --> pdb=" O GLU 8 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU 8 187 " --> pdb=" O LYS 8 183 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 8 192 " --> pdb=" O ASN 8 188 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP 8 194 " --> pdb=" O GLY 8 190 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU 8 195 " --> pdb=" O ALA 8 191 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG 8 198 " --> pdb=" O ASP 8 194 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 8 199 " --> pdb=" O GLU 8 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.623A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.158A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 216' Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.243A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.912A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.629A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.549A pdb=" N HIS D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.094A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.559A pdb=" N GLY D 46 " --> pdb=" O THR D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.888A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.597A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.938A pdb=" N ALA E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.556A pdb=" N ALA E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 4.161A pdb=" N SER E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.524A pdb=" N VAL E 194 " --> pdb=" O ASN E 190 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.534A pdb=" N ASN E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 removed outlier: 3.625A pdb=" N SER F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 5.818A pdb=" N ASP F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 54' Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.647A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.549A pdb=" N ASP F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.602A pdb=" N LEU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.615A pdb=" N ARG G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.726A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.935A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 22 through 29' Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.967A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.615A pdb=" N LEU J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 71 removed outlier: 3.943A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.616A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.772A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.247A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.673A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 38 through 43 removed outlier: 3.982A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.785A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.709A pdb=" N ILE L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN L 83 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.865A pdb=" N ALA L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.660A pdb=" N ARG L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.543A pdb=" N ILE M 47 " --> pdb=" O THR M 43 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.629A pdb=" N THR M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS M 123 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.559A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.334A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.664A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.536A pdb=" N LYS N 68 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 3.535A pdb=" N HIS N 77 " --> pdb=" O LYS N 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.872A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 3.752A pdb=" N ARG O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 3.535A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.723A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.939A pdb=" N GLU O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.660A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 97 through 103 removed outlier: 5.012A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.547A pdb=" N HIS Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG Q 15 " --> pdb=" O HIS Q 11 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.016A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU Q 31 " --> pdb=" O GLN Q 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 26 through 31' Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.529A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 47 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.562A pdb=" N ILE Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.558A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 removed outlier: 3.732A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.621A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.929A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 3.905A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.776A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.117A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN S 71 " --> pdb=" O ASN S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.738A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.623A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 51 removed outlier: 3.583A pdb=" N ILE T 42 " --> pdb=" O ASN T 38 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.211A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.567A pdb=" N SER V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA V 28 " --> pdb=" O ARG V 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY V 29 " --> pdb=" O ALA V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 59 removed outlier: 5.493A pdb=" N TYR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA V 54 " --> pdb=" O HIS V 50 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER V 59 " --> pdb=" O VAL V 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 3.635A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 3.686A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 13' Processing helix chain 'Y' and resid 14 through 39 removed outlier: 6.087A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU Y 24 " --> pdb=" O GLU Y 20 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN Y 35 " --> pdb=" O ASN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.628A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE Y 57 " --> pdb=" O GLU Y 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL Y 60 " --> pdb=" O ARG Y 56 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.838A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY Z 27 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.540A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.598A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.629A pdb=" N TYR c 31 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 3.818A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 72 through 77' Processing helix chain 'c' and resid 81 through 95 removed outlier: 4.682A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU c 93 " --> pdb=" O ASP c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.002A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.852A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.503A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.751A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 5.776A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.511A pdb=" N LEU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU d 52 " --> pdb=" O LEU d 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.693A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.406A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.713A pdb=" N TYR d 98 " --> pdb=" O ASP d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.517A pdb=" N GLN d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU d 112 " --> pdb=" O MET d 108 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.409A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 removed outlier: 6.328A pdb=" N ILE d 186 " --> pdb=" O GLU d 182 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 182 through 187' Processing helix chain 'd' and resid 192 through 201 removed outlier: 4.010A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU d 197 " --> pdb=" O GLN d 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 4.130A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.329A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.584A pdb=" N VAL e 168 " --> pdb=" O ALA e 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.787A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 3.871A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA e 196 " --> pdb=" O ILE e 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 191 through 196' Processing helix chain 'e' and resid 197 through 209 removed outlier: 3.570A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU e 208 " --> pdb=" O ARG e 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.656A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.087A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 4.069A pdb=" N GLU f 74 " --> pdb=" O ALA f 70 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.036A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.684A pdb=" N VAL g 43 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.639A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.633A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG g 112 " --> pdb=" O SER g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.643A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.687A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.553A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.523A pdb=" N GLN h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.573A pdb=" N ARG h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.780A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN i 67 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 3.685A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.608A pdb=" N ARG i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.711A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 24 removed outlier: 4.262A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 33 removed outlier: 4.614A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 26 through 33' Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.371A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 3.843A pdb=" N VAL k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 61' Processing helix chain 'k' and resid 64 through 69 removed outlier: 4.768A pdb=" N SER k 68 " --> pdb=" O GLY k 64 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR k 69 " --> pdb=" O SER k 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 64 through 69' Processing helix chain 'k' and resid 70 through 88 removed outlier: 3.512A pdb=" N GLN k 74 " --> pdb=" O PRO k 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU k 78 " --> pdb=" O GLN k 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP k 86 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.382A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.861A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.380A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.634A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.694A pdb=" N LEU m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA m 36 " --> pdb=" O GLU m 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.145A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 63 removed outlier: 3.844A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.690A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA m 76 " --> pdb=" O ARG m 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG m 79 " --> pdb=" O GLN m 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.553A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.505A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.596A pdb=" N ALA n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.875A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.992A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 5.196A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS o 44 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.921A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.568A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.555A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER p 61 " --> pdb=" O GLN p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.694A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 4.163A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.559A pdb=" N VAL p 105 " --> pdb=" O SER p 101 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU p 110 " --> pdb=" O PHE p 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA p 111 " --> pdb=" O ASN p 107 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.363A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 43 removed outlier: 4.958A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.697A pdb=" N ASP r 63 " --> pdb=" O GLN r 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.809A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN s 26 " --> pdb=" O GLN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.919A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 5 through 41 removed outlier: 3.709A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU t 15 " --> pdb=" O ASN t 11 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.094A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG t 56 " --> pdb=" O ALA t 52 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 60 " --> pdb=" O ARG t 56 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.700A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA t 78 " --> pdb=" O ASN t 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 43 through 53 removed outlier: 3.510A pdb=" N LEU x 48 " --> pdb=" O LYS x 44 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY x 53 " --> pdb=" O ARG x 49 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 92 removed outlier: 3.882A pdb=" N VAL x 89 " --> pdb=" O VAL x 85 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU x 90 " --> pdb=" O ARG x 86 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU x 91 " --> pdb=" O GLY x 87 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY x 92 " --> pdb=" O ASN x 88 " (cutoff:3.500A) Processing helix chain 'x' and resid 94 through 110 removed outlier: 4.360A pdb=" N ILE x 98 " --> pdb=" O GLY x 94 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS x 99 " --> pdb=" O ASP x 95 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU x 105 " --> pdb=" O ASP x 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU x 108 " --> pdb=" O ASN x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 114 through 133 removed outlier: 4.235A pdb=" N LEU x 118 " --> pdb=" O TYR x 114 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N MET x 119 " --> pdb=" O THR x 115 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU x 121 " --> pdb=" O GLU x 117 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU x 125 " --> pdb=" O GLU x 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN x 126 " --> pdb=" O MET x 122 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU x 128 " --> pdb=" O ARG x 124 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP x 130 " --> pdb=" O GLN x 126 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS x 131 " --> pdb=" O GLU x 127 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ALA x 132 " --> pdb=" O GLU x 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP x 133 " --> pdb=" O LEU x 129 " (cutoff:3.500A) Processing helix chain 'x' and resid 136 through 149 removed outlier: 3.565A pdb=" N LEU x 141 " --> pdb=" O LEU x 137 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP x 146 " --> pdb=" O GLU x 142 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU x 148 " --> pdb=" O ALA x 144 " (cutoff:3.500A) Processing helix chain 'x' and resid 161 through 177 removed outlier: 3.878A pdb=" N ARG x 165 " --> pdb=" O SER x 161 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG x 166 " --> pdb=" O GLY x 162 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA x 169 " --> pdb=" O ARG x 165 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS x 172 " --> pdb=" O VAL x 168 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU x 173 " --> pdb=" O ALA x 169 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER x 176 " --> pdb=" O LYS x 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS x 177 " --> pdb=" O LEU x 173 " (cutoff:3.500A) Processing helix chain 'x' and resid 191 through 205 removed outlier: 3.554A pdb=" N GLN x 200 " --> pdb=" O GLN x 196 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER x 204 " --> pdb=" O GLN x 200 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR x 205 " --> pdb=" O HIS x 201 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 223 removed outlier: 4.836A pdb=" N LEU x 219 " --> pdb=" O ASP x 215 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP x 220 " --> pdb=" O ARG x 216 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN x 221 " --> pdb=" O TYR x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 276 removed outlier: 6.091A pdb=" N TYR x 244 " --> pdb=" O ASN x 240 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU x 245 " --> pdb=" O TYR x 241 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU x 246 " --> pdb=" O SER x 242 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA x 253 " --> pdb=" O ALA x 249 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS x 261 " --> pdb=" O ARG x 257 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP x 272 " --> pdb=" O GLU x 268 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY x 276 " --> pdb=" O TRP x 272 " (cutoff:3.500A) Processing helix chain 'x' and resid 284 through 302 removed outlier: 4.128A pdb=" N ALA x 296 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU x 297 " --> pdb=" O GLU x 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU x 299 " --> pdb=" O ALA x 295 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS x 300 " --> pdb=" O ALA x 296 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR x 301 " --> pdb=" O GLU x 297 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG x 302 " --> pdb=" O ALA x 298 " (cutoff:3.500A) Processing helix chain 'x' and resid 359 through 369 removed outlier: 3.618A pdb=" N ILE x 367 " --> pdb=" O LEU x 363 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY x 369 " --> pdb=" O LYS x 365 " (cutoff:3.500A) Processing helix chain 'x' and resid 401 through 408 removed outlier: 3.626A pdb=" N VAL x 406 " --> pdb=" O VAL x 402 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP x 408 " --> pdb=" O GLU x 404 " (cutoff:3.500A) Processing helix chain 'x' and resid 421 through 430 removed outlier: 3.752A pdb=" N ALA x 428 " --> pdb=" O ALA x 424 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE x 429 " --> pdb=" O TYR x 425 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY x 430 " --> pdb=" O VAL x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 439 through 444 removed outlier: 3.541A pdb=" N LEU x 443 " --> pdb=" O PRO x 439 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER x 444 " --> pdb=" O ALA x 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 439 through 444' Processing helix chain 'x' and resid 445 through 460 removed outlier: 3.751A pdb=" N ARG x 450 " --> pdb=" O GLY x 446 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU x 451 " --> pdb=" O GLU x 447 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS x 458 " --> pdb=" O ALA x 454 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN x 459 " --> pdb=" O LEU x 455 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY x 460 " --> pdb=" O THR x 456 " (cutoff:3.500A) Processing helix chain 'x' and resid 474 through 488 removed outlier: 3.519A pdb=" N SER x 480 " --> pdb=" O GLU x 476 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA x 484 " --> pdb=" O SER x 480 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU x 486 " --> pdb=" O GLU x 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE x 488 " --> pdb=" O ALA x 484 " (cutoff:3.500A) Processing helix chain 'x' and resid 498 through 506 removed outlier: 4.548A pdb=" N ARG x 504 " --> pdb=" O TRP x 500 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR x 505 " --> pdb=" O PHE x 501 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS x 506 " --> pdb=" O LEU x 502 " (cutoff:3.500A) Processing helix chain 'x' and resid 528 through 540 removed outlier: 3.743A pdb=" N GLU x 534 " --> pdb=" O GLY x 530 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL x 537 " --> pdb=" O GLU x 533 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG x 539 " --> pdb=" O ASN x 535 " (cutoff:3.500A) Processing helix chain 'x' and resid 433 through 438 removed outlier: 3.568A pdb=" N GLN x 437 " --> pdb=" O PRO x 434 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 Processing sheet with id= 2, first strand: chain '1' and resid 10 through 13 removed outlier: 3.647A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 36 through 40 removed outlier: 6.592A pdb=" N LEU 1 36 " --> pdb=" O GLU 1 53 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.216A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '4' and resid 1 through 5 removed outlier: 3.844A pdb=" N GLY 4 37 " --> pdb=" O ASN 4 4 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '6' and resid 21 through 25 removed outlier: 4.982A pdb=" N GLY 6 31 " --> pdb=" O GLU 6 11 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 59 through 64 removed outlier: 6.501A pdb=" N VAL 8 59 " --> pdb=" O VAL 8 165 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE 8 161 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '8' and resid 94 through 97 removed outlier: 3.713A pdb=" N VAL 8 94 " --> pdb=" O VAL 8 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA 8 79 " --> pdb=" O GLY 8 96 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA 8 113 " --> pdb=" O ARG 8 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '8' and resid 169 through 176 removed outlier: 6.235A pdb=" N ALA 8 169 " --> pdb=" O LEU 8 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 8 48 " --> pdb=" O ALA 8 169 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.376A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.865A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 117 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY C 128 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU C 118 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.641A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.486A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 48 through 54 removed outlier: 5.487A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 172 through 178 removed outlier: 4.635A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 175 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 184 through 187 removed outlier: 3.517A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 112 through 116 Processing sheet with id= 19, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.558A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 13 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.526A pdb=" N ASP E 199 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 164 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.466A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG F 157 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU F 141 " --> pdb=" O ARG F 157 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 23 through 27 removed outlier: 3.572A pdb=" N LEU G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL G 26 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 41 through 46 removed outlier: 4.737A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 95 through 100 removed outlier: 3.600A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 100 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 122 through 127 removed outlier: 6.301A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY G 162 " --> pdb=" O PHE G 91 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.562A pdb=" N LYS H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.222A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.579A pdb=" N SER J 78 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.563A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.053A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 32, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.668A pdb=" N SER L 142 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 38 through 41 removed outlier: 6.764A pdb=" N GLU M 38 " --> pdb=" O PRO M 99 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 62 through 66 removed outlier: 4.097A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.996A pdb=" N ALA N 108 " --> pdb=" O ARG N 103 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET N 110 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.616A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 37 through 44 removed outlier: 3.542A pdb=" N VAL P 31 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.621A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 59 " --> pdb=" O ARG P 48 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.922A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL R 43 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR R 50 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 20 through 24 removed outlier: 4.115A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU R 34 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'R' and resid 67 through 71 removed outlier: 4.081A pdb=" N GLY R 67 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR R 69 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN R 93 " --> pdb=" O GLY R 71 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'R' and resid 73 through 79 Processing sheet with id= 43, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.861A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 83 through 89 removed outlier: 4.810A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 91 through 98 removed outlier: 4.278A pdb=" N ARG S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.359A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.865A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 49, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.902A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU V 9 " --> pdb=" O THR V 66 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 42 through 46 removed outlier: 3.529A pdb=" N ALA V 93 " --> pdb=" O PRO V 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 109 through 112 Processing sheet with id= 52, first strand: chain 'V' and resid 120 through 125 removed outlier: 7.569A pdb=" N VAL V 176 " --> pdb=" O GLU V 125 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL V 177 " --> pdb=" O LEU V 155 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR V 153 " --> pdb=" O VAL V 179 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 54, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.522A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.292A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.330A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 165 through 170 removed outlier: 3.504A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'd' and resid 135 through 139 removed outlier: 4.232A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TRP d 165 " --> pdb=" O HIS d 178 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.682A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.520A pdb=" N VAL e 125 " --> pdb=" O GLY e 118 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE e 154 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 63 through 72 removed outlier: 3.766A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.552A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR f 93 " --> pdb=" O PRO f 3 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 40 through 44 removed outlier: 5.836A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.364A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.382A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE h 62 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS h 58 " --> pdb=" O HIS h 29 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.565A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.606A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU i 42 " --> pdb=" O ILE i 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY i 31 " --> pdb=" O VAL i 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY i 89 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'j' and resid 69 through 76 removed outlier: 3.707A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE j 8 " --> pdb=" O ILE j 74 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG j 7 " --> pdb=" O GLN j 101 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 39 through 46 removed outlier: 4.092A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.173A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.969A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR l 38 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.424A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY p 38 " --> pdb=" O VAL p 20 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'q' and resid 59 through 63 removed outlier: 3.582A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 74 Processing sheet with id= 75, first strand: chain 's' and resid 48 through 52 Processing sheet with id= 76, first strand: chain 'x' and resid 6 through 9 Processing sheet with id= 77, first strand: chain 'x' and resid 69 through 74 removed outlier: 3.807A pdb=" N LEU x 180 " --> pdb=" O THR x 69 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA x 32 " --> pdb=" O GLY x 207 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU x 228 " --> pdb=" O TYR x 235 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG x 233 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'x' and resid 341 through 344 removed outlier: 4.373A pdb=" N VAL x 322 " --> pdb=" O LEU x 344 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL x 321 " --> pdb=" O GLY x 381 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY x 381 " --> pdb=" O VAL x 321 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 385 through 388 removed outlier: 3.726A pdb=" N GLY x 348 " --> pdb=" O GLY x 490 " (cutoff:3.500A) 1523 hydrogen bonds defined for protein. 4518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2949 hydrogen bonds 4744 hydrogen bond angles 0 basepair planarities 1207 basepair parallelities 2746 stacking parallelities Total time for adding SS restraints: 256.45 Time building geometry restraints manager: 64.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 13259 1.30 - 1.43: 73937 1.43 - 1.56: 68095 1.56 - 1.69: 9681 1.69 - 1.82: 170 Bond restraints: 165142 Sorted by residual: bond pdb=" C2' ANP x 602 " pdb=" C3' ANP x 602 " ideal model delta sigma weight residual 1.237 1.529 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C2' ANP x 601 " pdb=" C3' ANP x 601 " ideal model delta sigma weight residual 1.237 1.529 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.589 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 1.348 1.501 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 165137 not shown) Histogram of bond angle deviations from ideal: 98.20 - 106.18: 28918 106.18 - 114.16: 103656 114.16 - 122.14: 78891 122.14 - 130.12: 33581 130.12 - 138.10: 2125 Bond angle restraints: 247171 Sorted by residual: angle pdb=" C1' G7M a 518 " pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 94.96 127.23 -32.27 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 129.70 -21.41 3.00e+00 1.11e-01 5.09e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 122.13 20.69 3.00e+00 1.11e-01 4.76e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C8 2MG a 959 " ideal model delta sigma weight residual 110.07 128.83 -18.76 3.00e+00 1.11e-01 3.91e+01 angle pdb=" O3' G A2488 " pdb=" C3' G A2488 " pdb=" C2' G A2488 " ideal model delta sigma weight residual 109.50 118.39 -8.89 1.50e+00 4.44e-01 3.51e+01 ... (remaining 247166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 94845 35.73 - 71.46: 10049 71.46 - 107.19: 1322 107.19 - 142.92: 7 142.92 - 178.65: 30 Dihedral angle restraints: 106253 sinusoidal: 88721 harmonic: 17532 Sorted by residual: dihedral pdb=" O4' C A 739 " pdb=" C1' C A 739 " pdb=" N1 C A 739 " pdb=" C2 C A 739 " ideal model delta sinusoidal sigma weight residual 200.00 21.97 178.03 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 882 " pdb=" C1' C A 882 " pdb=" N1 C A 882 " pdb=" C2 C A 882 " ideal model delta sinusoidal sigma weight residual -160.00 15.51 -175.51 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A1517 " pdb=" C1' C A1517 " pdb=" N1 C A1517 " pdb=" C2 C A1517 " ideal model delta sinusoidal sigma weight residual 200.00 24.73 175.27 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 106250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 30141 0.103 - 0.205: 1316 0.205 - 0.308: 48 0.308 - 0.411: 6 0.411 - 0.513: 3 Chirality restraints: 31514 Sorted by residual: chirality pdb=" C3' G A2488 " pdb=" C4' G A2488 " pdb=" O3' G A2488 " pdb=" C2' G A2488 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CB VAL g 75 " pdb=" CA VAL g 75 " pdb=" CG1 VAL g 75 " pdb=" CG2 VAL g 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL Z 50 " pdb=" CA VAL Z 50 " pdb=" CG1 VAL Z 50 " pdb=" CG2 VAL Z 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 31511 not shown) Planarity restraints: 13410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.014 2.00e-02 2.50e+03 5.48e-01 6.77e+03 pdb=" C4' OMG A2791 " 0.426 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.602 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.588 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.528 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.223 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.879 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.813 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP x 602 " -0.208 2.00e-02 2.50e+03 5.48e-01 6.77e+03 pdb=" C2' ANP x 602 " 0.283 2.00e-02 2.50e+03 pdb=" C3' ANP x 602 " 0.599 2.00e-02 2.50e+03 pdb=" C4' ANP x 602 " -0.434 2.00e-02 2.50e+03 pdb=" C5' ANP x 602 " 0.035 2.00e-02 2.50e+03 pdb=" N9 ANP x 602 " 0.817 2.00e-02 2.50e+03 pdb=" O2' ANP x 602 " -0.771 2.00e-02 2.50e+03 pdb=" O3' ANP x 602 " 0.440 2.00e-02 2.50e+03 pdb=" O4' ANP x 602 " -0.762 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " -0.005 2.00e-02 2.50e+03 5.40e-01 6.56e+03 pdb=" C4' 2MG a 959 " 0.427 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.637 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.488 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.250 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.837 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.228 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.801 2.00e-02 2.50e+03 ... (remaining 13407 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 2133 2.59 - 3.17: 106667 3.17 - 3.74: 279137 3.74 - 4.32: 406710 4.32 - 4.90: 552910 Nonbonded interactions: 1347557 Sorted by model distance: nonbonded pdb=" OP1 C A 807 " pdb="MG MG A3203 " model vdw 2.009 2.170 nonbonded pdb=" OP2 G A1318 " pdb="MG MG A3287 " model vdw 2.012 2.170 nonbonded pdb=" OP2 A A1119 " pdb="MG MG A3287 " model vdw 2.015 2.170 nonbonded pdb=" OP1 C A 916 " pdb="MG MG A3264 " model vdw 2.017 2.170 nonbonded pdb=" OP1 A A2668 " pdb="MG MG A3273 " model vdw 2.020 2.170 ... (remaining 1347552 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: 1.990 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: 0.090 Extract box with map and model: 13.120 Check model and map are aligned: 1.620 Set scattering table: 1.050 Process input model: 578.340 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 613.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.292 165142 Z= 0.561 Angle : 0.878 32.274 247171 Z= 0.435 Chirality : 0.048 0.513 31514 Planarity : 0.013 0.548 13410 Dihedral : 22.153 178.648 94991 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.90 % Favored : 92.90 % Rotamer: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.08), residues: 6072 helix: -4.65 (0.05), residues: 1773 sheet: -1.95 (0.14), residues: 1159 loop : -2.57 (0.09), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP c 22 HIS 0.026 0.003 HIS M 13 PHE 0.044 0.004 PHE E 90 TYR 0.034 0.003 TYR C 6 ARG 0.028 0.002 ARG g 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1306 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 19 ARG cc_start: 0.8955 (ptp-170) cc_final: 0.8422 (ptm160) REVERT: 4 22 ARG cc_start: 0.8620 (ptp-110) cc_final: 0.8349 (ptp-170) REVERT: 8 20 LEU cc_start: 0.8717 (mt) cc_final: 0.8410 (mp) REVERT: 8 29 LEU cc_start: 0.8680 (mt) cc_final: 0.8293 (mp) REVERT: 8 51 ASP cc_start: 0.8429 (t0) cc_final: 0.8163 (t0) REVERT: 8 60 ARG cc_start: 0.7089 (ttm110) cc_final: 0.6866 (ttm-80) REVERT: 8 136 LEU cc_start: 0.8514 (mp) cc_final: 0.8233 (mp) REVERT: 8 151 LYS cc_start: 0.9055 (mttp) cc_final: 0.8607 (tttm) REVERT: 8 155 ASP cc_start: 0.8543 (m-30) cc_final: 0.8131 (m-30) REVERT: 8 199 LEU cc_start: 0.8241 (mm) cc_final: 0.8029 (mm) REVERT: C 44 ASN cc_start: 0.8407 (p0) cc_final: 0.8119 (p0) REVERT: C 181 GLU cc_start: 0.6962 (tp30) cc_final: 0.6531 (tp30) REVERT: C 261 ASN cc_start: 0.8617 (p0) cc_final: 0.8393 (p0) REVERT: D 138 SER cc_start: 0.8292 (t) cc_final: 0.8087 (t) REVERT: E 32 ASP cc_start: 0.8123 (t70) cc_final: 0.7763 (t0) REVERT: E 199 ASP cc_start: 0.7704 (m-30) cc_final: 0.7481 (m-30) REVERT: E 203 SER cc_start: 0.8118 (t) cc_final: 0.7897 (p) REVERT: F 84 PHE cc_start: 0.8574 (m-10) cc_final: 0.8348 (m-10) REVERT: F 101 ASP cc_start: 0.8555 (m-30) cc_final: 0.8320 (m-30) REVERT: F 108 ASP cc_start: 0.8574 (t0) cc_final: 0.8295 (t0) REVERT: F 160 ASP cc_start: 0.7661 (p0) cc_final: 0.7342 (p0) REVERT: G 84 TYR cc_start: 0.7962 (m-80) cc_final: 0.7568 (m-80) REVERT: J 24 VAL cc_start: 0.8651 (m) cc_final: 0.8399 (t) REVERT: J 108 MET cc_start: 0.8665 (mtt) cc_final: 0.8461 (mtt) REVERT: K 73 ASP cc_start: 0.7651 (p0) cc_final: 0.7423 (p0) REVERT: K 75 SER cc_start: 0.8748 (p) cc_final: 0.8522 (p) REVERT: M 25 THR cc_start: 0.9094 (p) cc_final: 0.8704 (t) REVERT: O 30 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7637 (ttm-80) REVERT: P 55 ARG cc_start: 0.8994 (ptp90) cc_final: 0.8563 (mtm-85) REVERT: Q 73 ASP cc_start: 0.6744 (p0) cc_final: 0.6528 (p0) REVERT: R 36 VAL cc_start: 0.8950 (m) cc_final: 0.8680 (p) REVERT: R 70 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8645 (mmtp) REVERT: S 30 VAL cc_start: 0.8849 (p) cc_final: 0.8614 (m) REVERT: T 4 LEU cc_start: 0.7270 (pt) cc_final: 0.6883 (tp) REVERT: T 62 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8364 (ttm170) REVERT: U 7 ASP cc_start: 0.7945 (m-30) cc_final: 0.7686 (m-30) REVERT: V 38 HIS cc_start: 0.7433 (m90) cc_final: 0.6959 (m170) REVERT: V 166 VAL cc_start: 0.8838 (t) cc_final: 0.8592 (m) REVERT: X 35 THR cc_start: 0.8714 (t) cc_final: 0.8459 (m) REVERT: Y 25 SER cc_start: 0.9100 (t) cc_final: 0.8806 (m) REVERT: Y 32 LEU cc_start: 0.9093 (mt) cc_final: 0.8795 (mm) REVERT: Z 9 VAL cc_start: 0.8828 (t) cc_final: 0.8571 (m) REVERT: c 17 ASP cc_start: 0.8119 (t70) cc_final: 0.7881 (t70) REVERT: c 188 GLU cc_start: 0.7614 (tt0) cc_final: 0.7310 (tt0) REVERT: c 191 THR cc_start: 0.8951 (t) cc_final: 0.8738 (p) REVERT: c 204 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8717 (mttm) REVERT: d 180 LEU cc_start: 0.8647 (mm) cc_final: 0.8371 (mt) REVERT: g 24 THR cc_start: 0.9199 (t) cc_final: 0.8901 (m) REVERT: g 143 LYS cc_start: 0.8400 (mttp) cc_final: 0.8029 (mtpt) REVERT: g 144 MET cc_start: 0.8417 (tpp) cc_final: 0.8138 (tpt) REVERT: h 81 SER cc_start: 0.8925 (t) cc_final: 0.8613 (t) REVERT: j 96 VAL cc_start: 0.8964 (t) cc_final: 0.8577 (p) REVERT: k 51 VAL cc_start: 0.8989 (t) cc_final: 0.8777 (m) REVERT: k 94 VAL cc_start: 0.8828 (t) cc_final: 0.8609 (m) REVERT: k 138 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8470 (mtp180) REVERT: m 75 GLN cc_start: 0.7875 (pp30) cc_final: 0.7598 (pp30) REVERT: q 117 ARG cc_start: 0.9148 (ptt90) cc_final: 0.8823 (ptt-90) REVERT: s 32 LYS cc_start: 0.8847 (tttp) cc_final: 0.8582 (ttmt) REVERT: t 22 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8151 (tttm) REVERT: t 60 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8138 (mtpp) REVERT: x 12 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6787 (ttt-90) REVERT: x 23 ASP cc_start: 0.7737 (t70) cc_final: 0.7159 (t70) REVERT: x 56 LYS cc_start: 0.8401 (mptp) cc_final: 0.7889 (mtmt) REVERT: x 155 GLU cc_start: 0.7671 (mp0) cc_final: 0.6992 (mp0) REVERT: x 244 TYR cc_start: 0.8064 (t80) cc_final: 0.7301 (t80) REVERT: x 289 GLN cc_start: 0.7529 (tt0) cc_final: 0.7305 (tm-30) REVERT: x 400 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8112 (mtpp) REVERT: x 404 GLU cc_start: 0.7809 (pt0) cc_final: 0.7482 (pt0) REVERT: x 411 ASP cc_start: 0.7500 (m-30) cc_final: 0.7158 (m-30) REVERT: x 427 SER cc_start: 0.8725 (p) cc_final: 0.8490 (m) REVERT: x 472 ASP cc_start: 0.6704 (m-30) cc_final: 0.6434 (m-30) outliers start: 6 outliers final: 3 residues processed: 1311 average time/residue: 2.5114 time to fit residues: 4564.7954 Evaluate side-chains 885 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 882 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 148 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain x residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 907 optimal weight: 10.0000 chunk 814 optimal weight: 9.9990 chunk 452 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 549 optimal weight: 1.9990 chunk 435 optimal weight: 7.9990 chunk 842 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 512 optimal weight: 4.9990 chunk 627 optimal weight: 6.9990 chunk 976 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 17 ASN 8 231 ASN C 70 ASN C 87 ASN C 164 GLN D 34 ASN D 179 ASN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 159 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN G 22 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN L 106 ASN P 79 ASN Q 44 ASN Q 77 ASN Q 122 ASN S 51 GLN V 44 HIS V 127 ASN X 37 HIS c 111 GLN c 176 HIS d 66 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 124 HIS d 151 GLN e 163 ASN i 65 HIS j 70 HIS l 109 ASN p 15 ASN q 70 GLN s 57 HIS x 104 ASN ** x 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 214 HIS ** x 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 518 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 165142 Z= 0.293 Angle : 0.664 19.706 247171 Z= 0.339 Chirality : 0.039 0.319 31514 Planarity : 0.006 0.123 13410 Dihedral : 23.006 179.466 83002 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.73 % Rotamer: Outliers : 3.29 % Allowed : 13.43 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.09), residues: 6072 helix: -2.88 (0.09), residues: 1857 sheet: -1.28 (0.15), residues: 1163 loop : -2.15 (0.10), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 22 HIS 0.010 0.001 HIS M 13 PHE 0.022 0.002 PHE i 85 TYR 0.025 0.002 TYR C 104 ARG 0.012 0.001 ARG i 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 976 time to evaluate : 6.400 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: 4 19 ARG cc_start: 0.9110 (ptp-170) cc_final: 0.8850 (ptp-170) REVERT: 4 22 ARG cc_start: 0.8636 (ptp-110) cc_final: 0.8376 (ptp-170) REVERT: 4 25 VAL cc_start: 0.8810 (t) cc_final: 0.8584 (p) REVERT: 6 1 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7392 (mtt) REVERT: 6 25 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7605 (ttp80) REVERT: 8 29 LEU cc_start: 0.8553 (mt) cc_final: 0.8251 (mp) REVERT: 8 51 ASP cc_start: 0.8444 (t0) cc_final: 0.8162 (t0) REVERT: 8 56 ASP cc_start: 0.8307 (m-30) cc_final: 0.7947 (p0) REVERT: 8 60 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6732 (ttp-110) REVERT: 8 112 ASP cc_start: 0.8763 (m-30) cc_final: 0.8329 (m-30) REVERT: 8 136 LEU cc_start: 0.8446 (mp) cc_final: 0.8197 (mp) REVERT: 8 151 LYS cc_start: 0.9065 (mttp) cc_final: 0.8620 (tttm) REVERT: 8 155 ASP cc_start: 0.8661 (m-30) cc_final: 0.8250 (m-30) REVERT: 8 167 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8990 (tppp) REVERT: 8 183 LYS cc_start: 0.8881 (mttp) cc_final: 0.7973 (tmmt) REVERT: 8 205 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8372 (mmtt) REVERT: C 44 ASN cc_start: 0.8509 (p0) cc_final: 0.8277 (p0) REVERT: C 177 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7895 (mtp) REVERT: C 261 ASN cc_start: 0.8628 (p0) cc_final: 0.8319 (p0) REVERT: E 10 LYS cc_start: 0.8184 (tptt) cc_final: 0.7797 (mmmt) REVERT: E 77 THR cc_start: 0.9109 (m) cc_final: 0.8889 (p) REVERT: E 127 ASN cc_start: 0.8979 (m110) cc_final: 0.8764 (m110) REVERT: F 108 ASP cc_start: 0.8344 (t0) cc_final: 0.8120 (t0) REVERT: G 19 ILE cc_start: 0.8130 (mt) cc_final: 0.7884 (mp) REVERT: G 84 TYR cc_start: 0.7902 (m-80) cc_final: 0.7549 (m-80) REVERT: J 86 LYS cc_start: 0.8666 (pttp) cc_final: 0.8427 (ptmm) REVERT: J 108 MET cc_start: 0.8834 (mtt) cc_final: 0.8548 (mtt) REVERT: K 5 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: M 25 THR cc_start: 0.9069 (p) cc_final: 0.8691 (t) REVERT: M 85 SER cc_start: 0.8648 (t) cc_final: 0.8365 (t) REVERT: O 30 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7426 (ttm-80) REVERT: P 55 ARG cc_start: 0.8970 (ptp90) cc_final: 0.8643 (mtm-85) REVERT: Q 73 ASP cc_start: 0.6887 (p0) cc_final: 0.6681 (p0) REVERT: Q 77 ASN cc_start: 0.7787 (t0) cc_final: 0.7579 (t160) REVERT: Q 89 GLU cc_start: 0.7698 (pt0) cc_final: 0.7472 (pt0) REVERT: R 88 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6890 (mtm180) REVERT: S 30 VAL cc_start: 0.8940 (p) cc_final: 0.8603 (m) REVERT: T 4 LEU cc_start: 0.7276 (pt) cc_final: 0.6899 (tp) REVERT: U 7 ASP cc_start: 0.7853 (m-30) cc_final: 0.7607 (m-30) REVERT: V 66 THR cc_start: 0.9145 (m) cc_final: 0.8592 (p) REVERT: V 126 THR cc_start: 0.8924 (m) cc_final: 0.8501 (t) REVERT: V 166 VAL cc_start: 0.8802 (t) cc_final: 0.8566 (m) REVERT: X 35 THR cc_start: 0.8754 (t) cc_final: 0.8491 (m) REVERT: Y 32 LEU cc_start: 0.8995 (mt) cc_final: 0.8696 (mm) REVERT: Z 16 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7815 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8156 (mtm-85) REVERT: c 4 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8519 (mttm) REVERT: c 17 ASP cc_start: 0.8093 (t70) cc_final: 0.7796 (t70) REVERT: c 57 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7099 (mt-10) REVERT: c 191 THR cc_start: 0.8662 (t) cc_final: 0.8437 (p) REVERT: d 64 GLU cc_start: 0.8217 (tp30) cc_final: 0.7826 (tp30) REVERT: e 151 VAL cc_start: 0.9031 (t) cc_final: 0.8827 (m) REVERT: g 24 THR cc_start: 0.8955 (t) cc_final: 0.8702 (m) REVERT: g 78 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7441 (ttt90) REVERT: g 123 GLU cc_start: 0.8298 (tp30) cc_final: 0.8078 (mm-30) REVERT: g 143 LYS cc_start: 0.8351 (mttp) cc_final: 0.7916 (mtpm) REVERT: h 43 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7918 (mm-30) REVERT: h 81 SER cc_start: 0.8922 (t) cc_final: 0.8613 (t) REVERT: i 94 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8972 (p) REVERT: i 121 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8656 (tptp) REVERT: i 151 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7105 (ptp-110) REVERT: j 63 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7858 (tt0) REVERT: k 94 VAL cc_start: 0.8717 (t) cc_final: 0.8423 (p) REVERT: l 21 THR cc_start: 0.8381 (t) cc_final: 0.8149 (m) REVERT: m 79 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7801 (tpm-80) REVERT: n 58 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8718 (mtpp) REVERT: p 39 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7895 (mtm-85) REVERT: t 5 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8836 (tttm) REVERT: t 22 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8074 (tttm) REVERT: x 12 ARG cc_start: 0.7110 (ttt-90) cc_final: 0.6841 (tmm-80) REVERT: x 23 ASP cc_start: 0.7813 (t70) cc_final: 0.7252 (t70) REVERT: x 56 LYS cc_start: 0.8458 (mptp) cc_final: 0.7940 (mtmt) REVERT: x 155 GLU cc_start: 0.7554 (mp0) cc_final: 0.7064 (mp0) REVERT: x 228 GLU cc_start: 0.8026 (tt0) cc_final: 0.7036 (mt-10) REVERT: x 400 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8124 (mtpp) REVERT: x 404 GLU cc_start: 0.7738 (pt0) cc_final: 0.7426 (pt0) REVERT: x 427 SER cc_start: 0.8651 (p) cc_final: 0.8413 (m) REVERT: x 438 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8396 (mttt) REVERT: x 472 ASP cc_start: 0.6546 (m-30) cc_final: 0.6332 (m-30) outliers start: 166 outliers final: 62 residues processed: 1059 average time/residue: 2.2709 time to fit residues: 3429.6772 Evaluate side-chains 945 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 869 time to evaluate : 6.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 ARG Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 167 LYS Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 226 ILE Chi-restraints excluded: chain x residue 248 LYS Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 542 optimal weight: 0.1980 chunk 302 optimal weight: 7.9990 chunk 812 optimal weight: 6.9990 chunk 664 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 977 optimal weight: 6.9990 chunk 1056 optimal weight: 4.9990 chunk 870 optimal weight: 9.9990 chunk 969 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 784 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 GLN d 54 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 153 HIS i 96 GLN l 109 ASN n 8 ASN q 70 GLN x 126 GLN x 189 HIS x 356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 165142 Z= 0.352 Angle : 0.651 18.335 247171 Z= 0.331 Chirality : 0.039 0.332 31514 Planarity : 0.006 0.123 13410 Dihedral : 22.871 179.610 83000 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.56 % Rotamer: Outliers : 4.25 % Allowed : 15.40 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 6072 helix: -1.86 (0.11), residues: 1862 sheet: -0.94 (0.15), residues: 1144 loop : -1.89 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 22 HIS 0.011 0.001 HIS M 13 PHE 0.021 0.002 PHE X 14 TYR 0.025 0.002 TYR C 104 ARG 0.012 0.001 ARG h 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 877 time to evaluate : 6.296 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: 4 22 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8407 (ptp-170) REVERT: 4 25 VAL cc_start: 0.8789 (t) cc_final: 0.8546 (p) REVERT: 8 29 LEU cc_start: 0.8505 (mt) cc_final: 0.8213 (mp) REVERT: 8 51 ASP cc_start: 0.8465 (t0) cc_final: 0.8206 (t0) REVERT: 8 136 LEU cc_start: 0.8448 (mp) cc_final: 0.8222 (mp) REVERT: 8 151 LYS cc_start: 0.9135 (mttp) cc_final: 0.8645 (tttm) REVERT: 8 155 ASP cc_start: 0.8553 (m-30) cc_final: 0.8203 (m-30) REVERT: 8 156 ILE cc_start: 0.8450 (mm) cc_final: 0.8173 (mp) REVERT: 8 225 ASP cc_start: 0.7694 (t0) cc_final: 0.7293 (t0) REVERT: C 261 ASN cc_start: 0.8630 (p0) cc_final: 0.8330 (p0) REVERT: D 133 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: E 10 LYS cc_start: 0.8376 (tptt) cc_final: 0.8025 (mtpt) REVERT: E 81 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8293 (ptt90) REVERT: F 71 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8442 (ttmm) REVERT: G 84 TYR cc_start: 0.7915 (m-80) cc_final: 0.7378 (m-80) REVERT: G 161 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: J 28 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8338 (tt) REVERT: J 108 MET cc_start: 0.8855 (mtt) cc_final: 0.8569 (mtt) REVERT: K 5 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: K 31 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7516 (mtp180) REVERT: M 25 THR cc_start: 0.9049 (p) cc_final: 0.8657 (t) REVERT: M 85 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8410 (t) REVERT: N 117 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.5847 (mtp85) REVERT: P 1 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7438 (ptp) REVERT: P 93 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8312 (mmt90) REVERT: P 103 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7998 (mtt-85) REVERT: Q 59 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8264 (ttmm) REVERT: Q 77 ASN cc_start: 0.7864 (t0) cc_final: 0.7650 (t0) REVERT: R 32 GLN cc_start: 0.8443 (tt0) cc_final: 0.8229 (tt0) REVERT: R 36 VAL cc_start: 0.8871 (m) cc_final: 0.8657 (p) REVERT: R 88 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.6855 (mtm180) REVERT: S 30 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8691 (m) REVERT: S 105 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7282 (mtp180) REVERT: T 4 LEU cc_start: 0.7280 (pt) cc_final: 0.6950 (tp) REVERT: U 7 ASP cc_start: 0.7884 (m-30) cc_final: 0.7602 (m-30) REVERT: U 79 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (mtmt) REVERT: V 87 ARG cc_start: 0.8642 (mtm110) cc_final: 0.8187 (mtm-85) REVERT: V 153 THR cc_start: 0.7712 (m) cc_final: 0.7396 (p) REVERT: V 166 VAL cc_start: 0.8857 (t) cc_final: 0.8580 (m) REVERT: X 35 THR cc_start: 0.8784 (t) cc_final: 0.8532 (m) REVERT: Y 32 LEU cc_start: 0.9046 (mt) cc_final: 0.8738 (mm) REVERT: Z 16 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7778 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8361 (mtm-85) REVERT: c 4 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: c 17 ASP cc_start: 0.8095 (t70) cc_final: 0.7785 (t70) REVERT: c 90 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7491 (mp) REVERT: c 106 LYS cc_start: 0.8363 (tptm) cc_final: 0.8142 (tppp) REVERT: d 64 GLU cc_start: 0.8242 (tp30) cc_final: 0.7873 (tp30) REVERT: e 60 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7858 (mtp85) REVERT: e 180 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7562 (mtt90) REVERT: f 7 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7977 (ttp) REVERT: f 86 LEU cc_start: 0.9002 (mt) cc_final: 0.8786 (mp) REVERT: g 4 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: g 78 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7444 (ttt90) REVERT: g 143 LYS cc_start: 0.8256 (mttp) cc_final: 0.7967 (mtpt) REVERT: g 144 MET cc_start: 0.8491 (tpp) cc_final: 0.8141 (tpt) REVERT: h 43 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7918 (mm-30) REVERT: i 94 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (p) REVERT: i 121 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8663 (tptp) REVERT: i 151 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7205 (ptp-110) REVERT: j 88 MET cc_start: 0.8167 (pmm) cc_final: 0.7944 (pmm) REVERT: k 94 VAL cc_start: 0.8678 (t) cc_final: 0.8379 (p) REVERT: k 129 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6853 (m110) REVERT: m 53 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8315 (mt) REVERT: m 56 LEU cc_start: 0.7658 (pp) cc_final: 0.7452 (pp) REVERT: m 93 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8274 (mtp85) REVERT: n 58 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (mtmt) REVERT: p 39 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (mtm-85) REVERT: p 84 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8367 (mptm) REVERT: q 68 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8805 (ptpp) REVERT: t 5 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8887 (tttp) REVERT: t 22 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8075 (tttm) REVERT: x 12 ARG cc_start: 0.7149 (ttt-90) cc_final: 0.6918 (tmm-80) REVERT: x 23 ASP cc_start: 0.7852 (t70) cc_final: 0.7313 (t70) REVERT: x 56 LYS cc_start: 0.8549 (mptp) cc_final: 0.7968 (mtmt) REVERT: x 93 MET cc_start: 0.7935 (mmm) cc_final: 0.7642 (mpm) REVERT: x 97 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6842 (ptmm) REVERT: x 105 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: x 122 MET cc_start: 0.7623 (ttt) cc_final: 0.7351 (ttt) REVERT: x 155 GLU cc_start: 0.7586 (mp0) cc_final: 0.6971 (mp0) REVERT: x 400 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7821 (mtpp) REVERT: x 427 SER cc_start: 0.8802 (p) cc_final: 0.8545 (m) outliers start: 214 outliers final: 99 residues processed: 1008 average time/residue: 2.1994 time to fit residues: 3193.8735 Evaluate side-chains 980 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 847 time to evaluate : 6.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 4 LYS Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 61 SER Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 82 ASP Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 105 GLU Chi-restraints excluded: chain x residue 161 SER Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 243 THR Chi-restraints excluded: chain x residue 362 THR Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 966 optimal weight: 3.9990 chunk 735 optimal weight: 8.9990 chunk 507 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 466 optimal weight: 10.0000 chunk 656 optimal weight: 0.9990 chunk 981 optimal weight: 8.9990 chunk 1039 optimal weight: 0.4980 chunk 512 optimal weight: 2.9990 chunk 930 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 165142 Z= 0.218 Angle : 0.592 17.337 247171 Z= 0.306 Chirality : 0.036 0.291 31514 Planarity : 0.005 0.119 13410 Dihedral : 22.901 179.173 82998 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 3.87 % Allowed : 16.92 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6072 helix: -1.34 (0.11), residues: 1861 sheet: -0.73 (0.16), residues: 1136 loop : -1.72 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 22 HIS 0.005 0.001 HIS M 13 PHE 0.044 0.002 PHE 6 22 TYR 0.017 0.001 TYR C 104 ARG 0.007 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 860 time to evaluate : 6.511 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: 1 8 ARG cc_start: 0.8884 (mtt-85) cc_final: 0.8643 (mtt-85) REVERT: 4 19 ARG cc_start: 0.8951 (ptp90) cc_final: 0.8213 (ptm160) REVERT: 4 25 VAL cc_start: 0.8763 (t) cc_final: 0.8536 (p) REVERT: 8 29 LEU cc_start: 0.8476 (mt) cc_final: 0.8199 (mp) REVERT: 8 51 ASP cc_start: 0.8448 (t0) cc_final: 0.8200 (t0) REVERT: 8 136 LEU cc_start: 0.8407 (mp) cc_final: 0.8196 (mp) REVERT: 8 151 LYS cc_start: 0.9157 (mttp) cc_final: 0.8591 (tttm) REVERT: 8 155 ASP cc_start: 0.8564 (m-30) cc_final: 0.8216 (m-30) REVERT: 8 156 ILE cc_start: 0.8418 (mm) cc_final: 0.8169 (mp) REVERT: 8 177 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7031 (tppp) REVERT: 8 225 ASP cc_start: 0.7753 (t0) cc_final: 0.7324 (t0) REVERT: C 26 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7673 (ttm-80) REVERT: C 261 ASN cc_start: 0.8621 (p0) cc_final: 0.8366 (p0) REVERT: D 133 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7772 (mtt-85) REVERT: E 10 LYS cc_start: 0.8359 (tptt) cc_final: 0.7984 (mtpp) REVERT: E 81 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8132 (ptt90) REVERT: E 158 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8114 (mtpp) REVERT: F 21 ASP cc_start: 0.8208 (m-30) cc_final: 0.7951 (m-30) REVERT: F 71 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8463 (ttmp) REVERT: F 87 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7724 (ptt-90) REVERT: F 160 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.6206 (p0) REVERT: G 84 TYR cc_start: 0.7855 (m-80) cc_final: 0.7328 (m-80) REVERT: G 161 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8754 (mtpt) REVERT: J 28 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8300 (tt) REVERT: J 86 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8461 (ptmm) REVERT: J 108 MET cc_start: 0.8859 (mtt) cc_final: 0.8610 (mtt) REVERT: K 5 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: K 31 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7494 (mtp180) REVERT: K 69 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7764 (tpt90) REVERT: M 25 THR cc_start: 0.9049 (p) cc_final: 0.8604 (t) REVERT: M 85 SER cc_start: 0.8640 (t) cc_final: 0.8359 (t) REVERT: N 71 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8037 (mtm-85) REVERT: N 117 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5842 (mtp85) REVERT: P 93 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8404 (mmt-90) REVERT: P 103 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7980 (mtt-85) REVERT: Q 77 ASN cc_start: 0.7810 (t0) cc_final: 0.7567 (t0) REVERT: R 36 VAL cc_start: 0.8878 (m) cc_final: 0.8674 (p) REVERT: R 88 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6851 (mtm180) REVERT: S 30 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8694 (m) REVERT: T 4 LEU cc_start: 0.7246 (pt) cc_final: 0.6933 (tp) REVERT: U 7 ASP cc_start: 0.7858 (m-30) cc_final: 0.7570 (m-30) REVERT: U 42 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: V 66 THR cc_start: 0.9183 (m) cc_final: 0.8707 (p) REVERT: V 87 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8172 (mtm-85) REVERT: V 113 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6960 (mm-30) REVERT: V 126 THR cc_start: 0.9051 (m) cc_final: 0.8483 (t) REVERT: V 153 THR cc_start: 0.7700 (m) cc_final: 0.7340 (p) REVERT: V 166 VAL cc_start: 0.8867 (t) cc_final: 0.8595 (m) REVERT: W 32 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8765 (mtpt) REVERT: X 35 THR cc_start: 0.8780 (t) cc_final: 0.8564 (m) REVERT: Y 32 LEU cc_start: 0.9038 (mt) cc_final: 0.8719 (mm) REVERT: Z 16 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7793 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8495 (mtm180) REVERT: c 4 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (mttp) REVERT: c 17 ASP cc_start: 0.8114 (t70) cc_final: 0.7795 (t70) REVERT: c 57 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7383 (mt-10) REVERT: c 58 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6960 (mtp85) REVERT: d 64 GLU cc_start: 0.8177 (tp30) cc_final: 0.7954 (tp30) REVERT: e 60 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7845 (mtp85) REVERT: e 180 ARG cc_start: 0.7748 (mtt90) cc_final: 0.7521 (mtt90) REVERT: f 7 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8023 (ttp) REVERT: f 86 LEU cc_start: 0.8961 (mt) cc_final: 0.8737 (mp) REVERT: g 4 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8178 (mtpt) REVERT: g 78 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7363 (ttt90) REVERT: g 143 LYS cc_start: 0.8231 (mttp) cc_final: 0.7929 (mtpt) REVERT: g 144 MET cc_start: 0.8475 (tpp) cc_final: 0.8117 (tpt) REVERT: h 43 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7880 (mm-30) REVERT: h 50 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8278 (ptt90) REVERT: h 63 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: h 93 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.7940 (p0) REVERT: i 48 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7073 (tttm) REVERT: i 94 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8961 (p) REVERT: i 121 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8669 (tptp) REVERT: i 151 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7129 (ptp-110) REVERT: j 88 MET cc_start: 0.8181 (pmm) cc_final: 0.7949 (pmm) REVERT: k 94 VAL cc_start: 0.8675 (t) cc_final: 0.8366 (p) REVERT: k 129 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6810 (m110) REVERT: m 53 LEU cc_start: 0.8521 (tp) cc_final: 0.8282 (mt) REVERT: n 58 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8687 (mmmt) REVERT: p 39 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7925 (mtm-85) REVERT: p 84 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8342 (mptm) REVERT: t 22 LYS cc_start: 0.8309 (ttpt) cc_final: 0.8056 (tttm) REVERT: x 12 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6919 (tmm-80) REVERT: x 23 ASP cc_start: 0.7820 (t70) cc_final: 0.7264 (t70) REVERT: x 56 LYS cc_start: 0.8525 (mptp) cc_final: 0.7952 (mtmt) REVERT: x 93 MET cc_start: 0.7924 (mmm) cc_final: 0.7433 (mpm) REVERT: x 97 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6816 (ptmm) REVERT: x 105 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: x 122 MET cc_start: 0.7462 (ttt) cc_final: 0.7245 (ttt) REVERT: x 136 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7123 (t70) REVERT: x 155 GLU cc_start: 0.7554 (mp0) cc_final: 0.6921 (mp0) REVERT: x 230 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: x 400 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7819 (mtpp) REVERT: x 427 SER cc_start: 0.8747 (p) cc_final: 0.8486 (m) REVERT: x 472 ASP cc_start: 0.6469 (m-30) cc_final: 0.6269 (m-30) outliers start: 195 outliers final: 97 residues processed: 972 average time/residue: 2.1832 time to fit residues: 3070.6420 Evaluate side-chains 966 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 829 time to evaluate : 6.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 23 GLN Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 205 LYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 4 LYS Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 50 ARG Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 93 ASN Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 63 LYS Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 105 GLU Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 482 GLU Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 865 optimal weight: 0.0570 chunk 589 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 773 optimal weight: 20.0000 chunk 428 optimal weight: 4.9990 chunk 886 optimal weight: 0.0470 chunk 718 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 530 optimal weight: 0.0980 chunk 932 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN E 47 GLN L 44 GLN L 106 ASN M 57 HIS ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN h 63 GLN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 165142 Z= 0.141 Angle : 0.545 17.124 247171 Z= 0.283 Chirality : 0.033 0.238 31514 Planarity : 0.005 0.117 13410 Dihedral : 22.883 178.947 82998 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.27 % Favored : 94.60 % Rotamer: Outliers : 3.31 % Allowed : 18.12 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 6072 helix: -0.72 (0.12), residues: 1849 sheet: -0.55 (0.16), residues: 1146 loop : -1.52 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 201 HIS 0.005 0.001 HIS P 28 PHE 0.019 0.001 PHE F 84 TYR 0.018 0.001 TYR h 21 ARG 0.016 0.001 ARG l 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 840 time to evaluate : 6.543 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: 8 29 LEU cc_start: 0.8460 (mt) cc_final: 0.8192 (mp) REVERT: 8 51 ASP cc_start: 0.8435 (t0) cc_final: 0.8109 (t0) REVERT: 8 112 ASP cc_start: 0.8768 (m-30) cc_final: 0.8368 (m-30) REVERT: 8 136 LEU cc_start: 0.8385 (mp) cc_final: 0.8159 (mp) REVERT: 8 151 LYS cc_start: 0.9163 (mttp) cc_final: 0.8608 (tttm) REVERT: 8 155 ASP cc_start: 0.8533 (m-30) cc_final: 0.8196 (m-30) REVERT: 8 177 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6980 (tppp) REVERT: 8 194 ASP cc_start: 0.8079 (t70) cc_final: 0.7733 (t70) REVERT: 8 225 ASP cc_start: 0.7740 (t0) cc_final: 0.7521 (m-30) REVERT: D 133 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7765 (mtt-85) REVERT: E 52 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7583 (mtp180) REVERT: E 158 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8136 (mtpp) REVERT: F 21 ASP cc_start: 0.8162 (m-30) cc_final: 0.7949 (m-30) REVERT: F 71 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8566 (ttmp) REVERT: G 84 TYR cc_start: 0.7816 (m-80) cc_final: 0.7291 (m-80) REVERT: J 28 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8276 (tt) REVERT: J 108 MET cc_start: 0.8849 (mtt) cc_final: 0.8581 (mtt) REVERT: K 5 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: K 31 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: L 94 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7679 (t) REVERT: M 25 THR cc_start: 0.9040 (p) cc_final: 0.8583 (t) REVERT: M 85 SER cc_start: 0.8563 (t) cc_final: 0.8332 (t) REVERT: N 71 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8020 (mtm-85) REVERT: N 117 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5740 (mtp85) REVERT: O 30 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7317 (ttm-80) REVERT: O 33 LEU cc_start: 0.8721 (tp) cc_final: 0.8508 (tt) REVERT: P 93 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (mmt-90) REVERT: P 103 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7980 (mtt-85) REVERT: Q 77 ASN cc_start: 0.7773 (t0) cc_final: 0.7557 (t0) REVERT: S 30 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8691 (m) REVERT: T 4 LEU cc_start: 0.7204 (pt) cc_final: 0.6931 (tp) REVERT: U 7 ASP cc_start: 0.7788 (m-30) cc_final: 0.7526 (m-30) REVERT: V 66 THR cc_start: 0.9192 (m) cc_final: 0.8773 (p) REVERT: V 87 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8182 (mtm-85) REVERT: V 113 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6950 (mm-30) REVERT: V 126 THR cc_start: 0.9048 (m) cc_final: 0.8824 (m) REVERT: V 166 VAL cc_start: 0.8857 (t) cc_final: 0.8588 (m) REVERT: Y 32 LEU cc_start: 0.9010 (mt) cc_final: 0.8704 (mm) REVERT: Z 16 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7757 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8452 (mtm180) REVERT: c 17 ASP cc_start: 0.8092 (t70) cc_final: 0.7771 (t70) REVERT: c 57 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7356 (mt-10) REVERT: c 111 GLN cc_start: 0.8594 (tp40) cc_final: 0.8107 (tp40) REVERT: e 60 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7786 (mtp180) REVERT: f 7 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: g 78 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7227 (ttt90) REVERT: g 79 ARG cc_start: 0.7196 (ttm-80) cc_final: 0.6813 (ttm-80) REVERT: g 143 LYS cc_start: 0.8232 (mttp) cc_final: 0.7926 (mtpt) REVERT: g 144 MET cc_start: 0.8474 (tpp) cc_final: 0.8119 (tpt) REVERT: h 43 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7889 (mm-30) REVERT: h 50 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (ptt90) REVERT: h 93 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.7906 (p0) REVERT: i 48 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7306 (ttpt) REVERT: i 94 SER cc_start: 0.9174 (t) cc_final: 0.8947 (p) REVERT: i 121 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8678 (tptp) REVERT: i 151 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7058 (ptp-110) REVERT: j 88 MET cc_start: 0.8204 (pmm) cc_final: 0.7976 (pmm) REVERT: k 90 ARG cc_start: 0.7907 (mmt-90) cc_final: 0.7496 (mmt-90) REVERT: k 94 VAL cc_start: 0.8646 (t) cc_final: 0.8332 (p) REVERT: k 129 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6736 (m110) REVERT: l 13 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.7103 (ttp-110) REVERT: o 79 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7884 (mpt-90) REVERT: p 84 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8380 (mptm) REVERT: q 110 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: t 22 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7995 (tttm) REVERT: x 12 ARG cc_start: 0.7157 (ttt-90) cc_final: 0.6919 (tmm-80) REVERT: x 23 ASP cc_start: 0.7779 (t70) cc_final: 0.7216 (t70) REVERT: x 56 LYS cc_start: 0.8523 (mptp) cc_final: 0.7944 (mtmt) REVERT: x 83 LYS cc_start: 0.8307 (mppt) cc_final: 0.8095 (ptmt) REVERT: x 93 MET cc_start: 0.7838 (mmm) cc_final: 0.7498 (mpm) REVERT: x 105 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: x 136 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6879 (t70) REVERT: x 155 GLU cc_start: 0.7551 (mp0) cc_final: 0.6857 (mp0) REVERT: x 230 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: x 266 LEU cc_start: 0.8731 (tp) cc_final: 0.8526 (tt) REVERT: x 400 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7650 (mtpp) REVERT: x 427 SER cc_start: 0.8673 (p) cc_final: 0.8407 (m) outliers start: 167 outliers final: 79 residues processed: 943 average time/residue: 2.1574 time to fit residues: 2958.7349 Evaluate side-chains 913 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 807 time to evaluate : 6.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain 8 residue 205 LYS Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 50 ARG Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 93 ASN Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 110 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 105 GLU Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 349 optimal weight: 10.0000 chunk 935 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 610 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 1040 optimal weight: 6.9990 chunk 863 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 chunk 86 optimal weight: 60.0000 chunk 344 optimal weight: 7.9990 chunk 546 optimal weight: 7.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 168 GLN D 179 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN h 63 GLN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 165142 Z= 0.422 Angle : 0.667 17.683 247171 Z= 0.334 Chirality : 0.040 0.340 31514 Planarity : 0.005 0.125 13410 Dihedral : 22.789 179.943 82998 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 3.93 % Allowed : 18.57 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 6072 helix: -0.72 (0.12), residues: 1858 sheet: -0.53 (0.15), residues: 1156 loop : -1.56 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 22 HIS 0.009 0.001 HIS M 13 PHE 0.029 0.002 PHE 6 22 TYR 0.021 0.002 TYR C 104 ARG 0.009 0.001 ARG h 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 815 time to evaluate : 6.658 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: 8 29 LEU cc_start: 0.8482 (mt) cc_final: 0.8200 (mp) REVERT: 8 51 ASP cc_start: 0.8433 (t0) cc_final: 0.8121 (t0) REVERT: 8 112 ASP cc_start: 0.8746 (m-30) cc_final: 0.8321 (m-30) REVERT: 8 115 ILE cc_start: 0.8351 (mp) cc_final: 0.7968 (pp) REVERT: 8 151 LYS cc_start: 0.9184 (mttp) cc_final: 0.8631 (tttm) REVERT: 8 155 ASP cc_start: 0.8542 (m-30) cc_final: 0.8240 (m-30) REVERT: 8 225 ASP cc_start: 0.7949 (t0) cc_final: 0.7626 (p0) REVERT: C 26 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7526 (ttm-80) REVERT: C 177 MET cc_start: 0.8605 (mmm) cc_final: 0.8368 (mpp) REVERT: D 133 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7775 (mtt-85) REVERT: E 81 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8391 (ptt90) REVERT: E 158 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: F 21 ASP cc_start: 0.8155 (m-30) cc_final: 0.7913 (m-30) REVERT: F 71 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8600 (ttmp) REVERT: F 87 ARG cc_start: 0.8389 (ptt-90) cc_final: 0.8082 (ptt-90) REVERT: G 161 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8677 (mtpt) REVERT: J 28 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8340 (tt) REVERT: J 94 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: J 108 MET cc_start: 0.8870 (mtt) cc_final: 0.8599 (mtt) REVERT: K 5 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: K 31 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: K 69 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7824 (tpt90) REVERT: M 25 THR cc_start: 0.9046 (p) cc_final: 0.8596 (t) REVERT: M 85 SER cc_start: 0.8706 (t) cc_final: 0.8422 (t) REVERT: N 71 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8081 (mtm-85) REVERT: N 117 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.5848 (mtp85) REVERT: P 93 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8340 (mmt90) REVERT: P 103 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8028 (mtt-85) REVERT: Q 51 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: Q 59 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8255 (ttmm) REVERT: R 88 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.6858 (mtm180) REVERT: S 30 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8705 (m) REVERT: S 105 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7267 (mtp180) REVERT: T 4 LEU cc_start: 0.7301 (pt) cc_final: 0.7009 (tp) REVERT: U 7 ASP cc_start: 0.7881 (m-30) cc_final: 0.7587 (m-30) REVERT: U 42 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7866 (mtmt) REVERT: V 66 THR cc_start: 0.9218 (m) cc_final: 0.8758 (p) REVERT: V 113 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6978 (mm-30) REVERT: V 126 THR cc_start: 0.9077 (m) cc_final: 0.8857 (m) REVERT: V 166 VAL cc_start: 0.8876 (t) cc_final: 0.8568 (m) REVERT: Y 48 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7749 (ttt-90) REVERT: Z 16 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7791 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8462 (mtm-85) REVERT: c 17 ASP cc_start: 0.8121 (t70) cc_final: 0.7786 (t70) REVERT: c 57 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7475 (mt-10) REVERT: d 87 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: e 60 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7851 (mtp180) REVERT: f 7 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: g 24 THR cc_start: 0.8956 (t) cc_final: 0.8690 (m) REVERT: g 78 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7374 (ttt90) REVERT: g 143 LYS cc_start: 0.8245 (mttp) cc_final: 0.7940 (mtpt) REVERT: g 144 MET cc_start: 0.8489 (tpp) cc_final: 0.8255 (tpt) REVERT: h 43 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7925 (mm-30) REVERT: i 48 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7498 (ttpt) REVERT: i 94 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8970 (p) REVERT: i 121 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8676 (tptp) REVERT: i 151 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7179 (ptp-110) REVERT: j 88 MET cc_start: 0.8208 (pmm) cc_final: 0.7971 (pmm) REVERT: k 90 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7465 (mmt-90) REVERT: k 129 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6867 (m110) REVERT: p 72 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7954 (mptm) REVERT: p 84 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8326 (mptm) REVERT: q 110 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7598 (mtp180) REVERT: t 22 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8069 (tttm) REVERT: x 12 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6892 (tmm-80) REVERT: x 23 ASP cc_start: 0.7813 (t70) cc_final: 0.7247 (t70) REVERT: x 56 LYS cc_start: 0.8575 (mptp) cc_final: 0.7981 (mtmt) REVERT: x 93 MET cc_start: 0.7837 (mmm) cc_final: 0.7635 (mmm) REVERT: x 97 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6864 (ptmm) REVERT: x 136 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7042 (t70) REVERT: x 155 GLU cc_start: 0.7547 (mp0) cc_final: 0.6815 (mp0) REVERT: x 230 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: x 400 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7715 (mtpp) REVERT: x 427 SER cc_start: 0.8767 (p) cc_final: 0.8544 (m) outliers start: 198 outliers final: 114 residues processed: 931 average time/residue: 2.1413 time to fit residues: 2905.3463 Evaluate side-chains 945 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 797 time to evaluate : 7.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 72 LYS Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 76 GLU Chi-restraints excluded: chain q residue 110 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 1002 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 592 optimal weight: 2.9990 chunk 759 optimal weight: 20.0000 chunk 588 optimal weight: 0.6980 chunk 875 optimal weight: 20.0000 chunk 580 optimal weight: 4.9990 chunk 1036 optimal weight: 6.9990 chunk 648 optimal weight: 9.9990 chunk 631 optimal weight: 20.0000 chunk 478 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN F 134 ASN L 106 ASN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 165142 Z= 0.282 Angle : 0.618 17.556 247171 Z= 0.315 Chirality : 0.037 0.316 31514 Planarity : 0.005 0.122 13410 Dihedral : 22.821 179.412 82998 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 3.97 % Allowed : 19.25 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 6072 helix: -0.60 (0.12), residues: 1856 sheet: -0.51 (0.15), residues: 1160 loop : -1.53 (0.11), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 22 HIS 0.007 0.001 HIS M 13 PHE 0.031 0.002 PHE 6 22 TYR 0.018 0.002 TYR C 104 ARG 0.013 0.001 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 800 time to evaluate : 6.490 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: 8 29 LEU cc_start: 0.8474 (mt) cc_final: 0.8188 (mp) REVERT: 8 51 ASP cc_start: 0.8418 (t0) cc_final: 0.8100 (t0) REVERT: 8 112 ASP cc_start: 0.8749 (m-30) cc_final: 0.8299 (m-30) REVERT: 8 115 ILE cc_start: 0.8346 (mp) cc_final: 0.7985 (pp) REVERT: 8 151 LYS cc_start: 0.9164 (mttp) cc_final: 0.8602 (tttm) REVERT: 8 155 ASP cc_start: 0.8534 (m-30) cc_final: 0.8229 (m-30) REVERT: 8 177 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7034 (tppp) REVERT: 8 194 ASP cc_start: 0.8164 (t70) cc_final: 0.7810 (t70) REVERT: 8 225 ASP cc_start: 0.7947 (t0) cc_final: 0.7615 (p0) REVERT: C 26 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7553 (ttm-80) REVERT: C 177 MET cc_start: 0.8601 (mmm) cc_final: 0.8364 (mpp) REVERT: D 133 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7771 (mtt-85) REVERT: E 81 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8294 (ptt90) REVERT: E 158 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: F 21 ASP cc_start: 0.8143 (m-30) cc_final: 0.7906 (m-30) REVERT: F 71 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8578 (ttmp) REVERT: G 161 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8673 (mtpt) REVERT: J 28 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8302 (tt) REVERT: J 94 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: J 108 MET cc_start: 0.8866 (mtt) cc_final: 0.8594 (mtt) REVERT: K 5 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: K 31 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: M 25 THR cc_start: 0.9036 (p) cc_final: 0.8602 (t) REVERT: M 85 SER cc_start: 0.8670 (t) cc_final: 0.8387 (t) REVERT: N 71 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: N 117 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.5833 (mtp85) REVERT: P 93 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8282 (mmt90) REVERT: P 103 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8016 (mtt-85) REVERT: Q 51 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6832 (mtp180) REVERT: Q 59 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: R 88 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6846 (mtm180) REVERT: S 30 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8703 (m) REVERT: S 105 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7278 (mtp180) REVERT: T 4 LEU cc_start: 0.7281 (pt) cc_final: 0.7010 (tp) REVERT: U 7 ASP cc_start: 0.7870 (m-30) cc_final: 0.7565 (m-30) REVERT: U 42 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7861 (mtmt) REVERT: V 66 THR cc_start: 0.9216 (m) cc_final: 0.8760 (p) REVERT: V 87 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8364 (mtt90) REVERT: V 99 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6531 (ttm110) REVERT: V 113 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6967 (mm-30) REVERT: V 126 THR cc_start: 0.9068 (m) cc_final: 0.8852 (m) REVERT: V 166 VAL cc_start: 0.8876 (t) cc_final: 0.8568 (m) REVERT: X 27 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8733 (ptm160) REVERT: Z 16 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7750 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8369 (mtm-85) REVERT: c 17 ASP cc_start: 0.8105 (t70) cc_final: 0.7776 (t70) REVERT: c 57 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7476 (mt-10) REVERT: d 87 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8206 (ttpp) REVERT: e 60 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: f 7 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: g 24 THR cc_start: 0.8940 (t) cc_final: 0.8673 (m) REVERT: g 78 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7368 (ttt90) REVERT: g 143 LYS cc_start: 0.8255 (mttp) cc_final: 0.7946 (mtpt) REVERT: g 144 MET cc_start: 0.8473 (tpp) cc_final: 0.8249 (tpt) REVERT: h 43 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7892 (mm-30) REVERT: i 28 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: i 48 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7482 (ttpt) REVERT: i 94 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8963 (p) REVERT: i 121 LYS cc_start: 0.9140 (ttpp) cc_final: 0.8674 (tptp) REVERT: i 151 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7162 (ptp-110) REVERT: j 88 MET cc_start: 0.8205 (pmm) cc_final: 0.7965 (pmm) REVERT: k 129 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6843 (m110) REVERT: p 72 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (mptm) REVERT: p 84 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8315 (mptm) REVERT: q 110 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7603 (mtp180) REVERT: t 22 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8051 (tttm) REVERT: x 12 ARG cc_start: 0.7084 (ttt-90) cc_final: 0.6839 (tmm-80) REVERT: x 23 ASP cc_start: 0.7809 (t70) cc_final: 0.7241 (t70) REVERT: x 56 LYS cc_start: 0.8576 (mptp) cc_final: 0.7978 (mtmt) REVERT: x 93 MET cc_start: 0.7813 (mmm) cc_final: 0.7270 (mpm) REVERT: x 97 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6872 (ptmm) REVERT: x 136 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7040 (t70) REVERT: x 155 GLU cc_start: 0.7564 (mp0) cc_final: 0.6846 (mp0) REVERT: x 230 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: x 400 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7708 (mtpp) REVERT: x 427 SER cc_start: 0.8720 (p) cc_final: 0.8490 (m) outliers start: 200 outliers final: 131 residues processed: 916 average time/residue: 2.1493 time to fit residues: 2866.6414 Evaluate side-chains 965 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 796 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 63 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 103 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 99 ARG Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 28 GLN Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 61 SER Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 72 LYS Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 110 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 119 MET Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 362 THR Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 641 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 618 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 658 optimal weight: 2.9990 chunk 705 optimal weight: 10.0000 chunk 512 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 814 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN L 106 ASN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 HIS ** x 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 165142 Z= 0.247 Angle : 0.599 17.376 247171 Z= 0.306 Chirality : 0.036 0.299 31514 Planarity : 0.005 0.121 13410 Dihedral : 22.824 179.361 82998 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 3.77 % Allowed : 19.33 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 6072 helix: -0.49 (0.12), residues: 1858 sheet: -0.47 (0.15), residues: 1161 loop : -1.50 (0.11), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 22 HIS 0.010 0.001 HIS p 41 PHE 0.031 0.002 PHE 6 22 TYR 0.018 0.001 TYR 1 23 ARG 0.011 0.000 ARG l 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 804 time to evaluate : 6.530 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: 8 29 LEU cc_start: 0.8472 (mt) cc_final: 0.8187 (mp) REVERT: 8 51 ASP cc_start: 0.8414 (t0) cc_final: 0.8097 (t0) REVERT: 8 115 ILE cc_start: 0.8490 (mp) cc_final: 0.8127 (pp) REVERT: 8 151 LYS cc_start: 0.9166 (mttp) cc_final: 0.8599 (tttm) REVERT: 8 155 ASP cc_start: 0.8545 (m-30) cc_final: 0.8231 (m-30) REVERT: 8 177 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6999 (tppp) REVERT: 8 194 ASP cc_start: 0.8152 (t70) cc_final: 0.7799 (t70) REVERT: 8 205 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8578 (mmmt) REVERT: 8 225 ASP cc_start: 0.7948 (t0) cc_final: 0.7613 (p0) REVERT: C 26 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7556 (ttm-80) REVERT: D 133 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: E 52 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: E 79 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8053 (mtp85) REVERT: E 81 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8284 (ptt90) REVERT: E 158 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8141 (mtpp) REVERT: F 21 ASP cc_start: 0.8135 (m-30) cc_final: 0.7905 (m-30) REVERT: F 71 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8575 (ttmp) REVERT: F 87 ARG cc_start: 0.8376 (ptt-90) cc_final: 0.8060 (ptt-90) REVERT: G 161 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8698 (mtpt) REVERT: J 28 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8293 (tt) REVERT: J 94 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: J 108 MET cc_start: 0.8865 (mtt) cc_final: 0.8608 (mtt) REVERT: K 5 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: K 31 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7504 (mtp180) REVERT: M 25 THR cc_start: 0.9035 (p) cc_final: 0.8600 (t) REVERT: M 85 SER cc_start: 0.8656 (t) cc_final: 0.8383 (t) REVERT: N 71 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8047 (mtm-85) REVERT: N 117 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.5857 (mtp85) REVERT: P 93 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8282 (mmt90) REVERT: Q 51 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6815 (mtp180) REVERT: Q 59 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8244 (ttmm) REVERT: R 88 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.6842 (mtm180) REVERT: S 30 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8703 (m) REVERT: S 105 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7278 (mtp180) REVERT: T 4 LEU cc_start: 0.7247 (pt) cc_final: 0.6978 (tp) REVERT: U 7 ASP cc_start: 0.7866 (m-30) cc_final: 0.7564 (m-30) REVERT: U 42 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7842 (mtmt) REVERT: V 66 THR cc_start: 0.9211 (m) cc_final: 0.8754 (p) REVERT: V 87 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8359 (mtt90) REVERT: V 99 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6529 (ttm110) REVERT: V 113 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6961 (mm-30) REVERT: V 126 THR cc_start: 0.9068 (m) cc_final: 0.8849 (m) REVERT: V 166 VAL cc_start: 0.8871 (t) cc_final: 0.8562 (m) REVERT: X 27 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8746 (ptm160) REVERT: Z 16 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7758 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8302 (mtm-85) REVERT: c 17 ASP cc_start: 0.8104 (t70) cc_final: 0.7775 (t70) REVERT: c 57 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7486 (mt-10) REVERT: d 87 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8208 (ttpp) REVERT: e 60 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7795 (mtp180) REVERT: f 7 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8089 (ttp) REVERT: g 24 THR cc_start: 0.8924 (t) cc_final: 0.8668 (m) REVERT: g 78 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7333 (ttt90) REVERT: g 143 LYS cc_start: 0.8238 (mttp) cc_final: 0.7932 (mtpt) REVERT: g 144 MET cc_start: 0.8473 (tpp) cc_final: 0.8250 (tpt) REVERT: h 43 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7909 (mm-30) REVERT: i 48 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7459 (ttpt) REVERT: i 94 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8960 (p) REVERT: i 121 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8671 (tptp) REVERT: i 151 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7148 (ptp-110) REVERT: j 88 MET cc_start: 0.8202 (pmm) cc_final: 0.7968 (pmm) REVERT: k 90 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7622 (mmt-90) REVERT: k 129 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6832 (m110) REVERT: l 79 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7303 (mmm) REVERT: p 72 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7973 (mptm) REVERT: p 84 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8372 (mptm) REVERT: q 110 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7588 (mtp180) REVERT: t 22 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8048 (tttm) REVERT: x 12 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6830 (tmm-80) REVERT: x 23 ASP cc_start: 0.7802 (t70) cc_final: 0.7230 (t70) REVERT: x 56 LYS cc_start: 0.8577 (mptp) cc_final: 0.7976 (mtmt) REVERT: x 93 MET cc_start: 0.7761 (mmm) cc_final: 0.7294 (mpm) REVERT: x 97 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6977 (ptmm) REVERT: x 136 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7015 (t70) REVERT: x 155 GLU cc_start: 0.7558 (mp0) cc_final: 0.6831 (mp0) REVERT: x 230 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: x 400 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7711 (mtpp) REVERT: x 427 SER cc_start: 0.8682 (p) cc_final: 0.8445 (m) outliers start: 190 outliers final: 122 residues processed: 918 average time/residue: 2.1117 time to fit residues: 2821.9847 Evaluate side-chains 957 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 796 time to evaluate : 6.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 18 SER Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 63 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 99 ARG Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain m residue 90 LEU Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 72 LYS Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 110 ARG Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 362 THR Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 942 optimal weight: 4.9990 chunk 992 optimal weight: 3.9990 chunk 905 optimal weight: 0.7980 chunk 965 optimal weight: 9.9990 chunk 581 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 758 optimal weight: 30.0000 chunk 296 optimal weight: 10.0000 chunk 872 optimal weight: 9.9990 chunk 913 optimal weight: 9.9990 chunk 962 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN L 106 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 165142 Z= 0.215 Angle : 0.590 17.352 247171 Z= 0.303 Chirality : 0.035 0.291 31514 Planarity : 0.005 0.121 13410 Dihedral : 22.831 179.231 82998 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 3.51 % Allowed : 19.66 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.11), residues: 6072 helix: -0.40 (0.12), residues: 1857 sheet: -0.48 (0.15), residues: 1162 loop : -1.47 (0.11), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 201 HIS 0.005 0.001 HIS S 112 PHE 0.026 0.001 PHE F 84 TYR 0.017 0.001 TYR 8 189 ARG 0.012 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 792 time to evaluate : 6.555 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: 8 29 LEU cc_start: 0.8459 (mt) cc_final: 0.8164 (mp) REVERT: 8 51 ASP cc_start: 0.8408 (t0) cc_final: 0.8093 (t0) REVERT: 8 112 ASP cc_start: 0.8737 (m-30) cc_final: 0.8343 (m-30) REVERT: 8 115 ILE cc_start: 0.8367 (mp) cc_final: 0.8008 (pp) REVERT: 8 151 LYS cc_start: 0.9168 (mttp) cc_final: 0.8596 (tttm) REVERT: 8 155 ASP cc_start: 0.8544 (m-30) cc_final: 0.8226 (m-30) REVERT: 8 177 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6960 (tppp) REVERT: 8 194 ASP cc_start: 0.8144 (t70) cc_final: 0.7790 (t70) REVERT: 8 205 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8579 (mmmt) REVERT: 8 225 ASP cc_start: 0.7958 (t0) cc_final: 0.7618 (p0) REVERT: C 26 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7527 (ttm-80) REVERT: D 133 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: E 52 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7457 (mtp180) REVERT: E 79 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8049 (mtp85) REVERT: E 81 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8307 (ptt90) REVERT: E 158 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8150 (mtpp) REVERT: F 21 ASP cc_start: 0.8131 (m-30) cc_final: 0.7905 (m-30) REVERT: F 71 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8569 (ttmp) REVERT: F 87 ARG cc_start: 0.8333 (ptt-90) cc_final: 0.8058 (ptt-90) REVERT: G 161 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8696 (mtpt) REVERT: J 28 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8290 (tt) REVERT: J 94 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: J 108 MET cc_start: 0.8868 (mtt) cc_final: 0.8607 (mtt) REVERT: K 5 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: K 31 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: M 25 THR cc_start: 0.9031 (p) cc_final: 0.8598 (t) REVERT: M 85 SER cc_start: 0.8645 (t) cc_final: 0.8380 (t) REVERT: N 71 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8038 (mtm-85) REVERT: N 117 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5852 (mtp85) REVERT: P 93 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8265 (mmt90) REVERT: Q 51 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.6806 (mtp180) REVERT: Q 59 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8270 (ttmm) REVERT: R 88 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6825 (mtm180) REVERT: S 30 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8703 (m) REVERT: S 105 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7280 (mtp180) REVERT: T 4 LEU cc_start: 0.7206 (pt) cc_final: 0.6949 (tp) REVERT: U 7 ASP cc_start: 0.7858 (m-30) cc_final: 0.7548 (m-30) REVERT: U 42 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7838 (mtmt) REVERT: V 66 THR cc_start: 0.9211 (m) cc_final: 0.8760 (p) REVERT: V 87 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8357 (mtt90) REVERT: V 99 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6516 (ttm110) REVERT: V 113 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6983 (mm-30) REVERT: V 166 VAL cc_start: 0.8867 (t) cc_final: 0.8554 (m) REVERT: X 27 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (ptt90) REVERT: Z 16 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7749 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8299 (mtm-85) REVERT: c 17 ASP cc_start: 0.8135 (t70) cc_final: 0.7809 (t70) REVERT: c 57 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7473 (mt-10) REVERT: c 111 GLN cc_start: 0.8609 (tp40) cc_final: 0.8151 (tp40) REVERT: d 87 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: e 60 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: f 7 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8078 (ttp) REVERT: g 24 THR cc_start: 0.8919 (t) cc_final: 0.8662 (m) REVERT: g 78 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7315 (ttt90) REVERT: g 143 LYS cc_start: 0.8231 (mttp) cc_final: 0.7926 (mtpt) REVERT: g 144 MET cc_start: 0.8459 (tpp) cc_final: 0.8239 (tpt) REVERT: h 43 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7914 (mm-30) REVERT: i 48 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7454 (ttpt) REVERT: i 94 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8957 (p) REVERT: i 121 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8686 (tptp) REVERT: i 151 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7136 (ptp-110) REVERT: j 88 MET cc_start: 0.8200 (pmm) cc_final: 0.7963 (pmm) REVERT: k 90 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7622 (mmt-90) REVERT: k 129 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6828 (m110) REVERT: p 72 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7984 (mptm) REVERT: p 84 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8413 (mptm) REVERT: t 22 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8042 (tttm) REVERT: x 12 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6816 (tmm-80) REVERT: x 23 ASP cc_start: 0.7796 (t70) cc_final: 0.7225 (t70) REVERT: x 56 LYS cc_start: 0.8577 (mptp) cc_final: 0.7975 (mtmt) REVERT: x 93 MET cc_start: 0.7789 (mmm) cc_final: 0.7239 (mpm) REVERT: x 97 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6979 (ptmm) REVERT: x 136 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6982 (t70) REVERT: x 155 GLU cc_start: 0.7557 (mp0) cc_final: 0.6826 (mp0) REVERT: x 230 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: x 400 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7703 (mtpp) REVERT: x 427 SER cc_start: 0.8675 (p) cc_final: 0.8439 (m) outliers start: 177 outliers final: 123 residues processed: 895 average time/residue: 2.1862 time to fit residues: 2864.5595 Evaluate side-chains 945 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 785 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 63 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 99 ARG Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 90 LEU Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 72 LYS Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 115 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 362 THR Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 634 optimal weight: 4.9990 chunk 1020 optimal weight: 0.0370 chunk 623 optimal weight: 0.6980 chunk 484 optimal weight: 2.9990 chunk 709 optimal weight: 10.0000 chunk 1070 optimal weight: 10.0000 chunk 985 optimal weight: 10.0000 chunk 852 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 658 optimal weight: 1.9990 chunk 522 optimal weight: 7.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN L 106 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 165142 Z= 0.181 Angle : 0.575 17.354 247171 Z= 0.296 Chirality : 0.034 0.275 31514 Planarity : 0.005 0.120 13410 Dihedral : 22.840 179.099 82998 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.83 % Favored : 94.05 % Rotamer: Outliers : 3.25 % Allowed : 19.94 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 6072 helix: -0.26 (0.12), residues: 1843 sheet: -0.43 (0.16), residues: 1157 loop : -1.42 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 201 HIS 0.004 0.001 HIS S 112 PHE 0.060 0.001 PHE 6 22 TYR 0.019 0.001 TYR T 73 ARG 0.012 0.000 ARG h 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 797 time to evaluate : 6.537 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: 8 29 LEU cc_start: 0.8462 (mt) cc_final: 0.8188 (mp) REVERT: 8 51 ASP cc_start: 0.8405 (t0) cc_final: 0.8089 (t0) REVERT: 8 115 ILE cc_start: 0.8514 (mp) cc_final: 0.8181 (pp) REVERT: 8 151 LYS cc_start: 0.9166 (mttp) cc_final: 0.8595 (tttm) REVERT: 8 155 ASP cc_start: 0.8499 (m-30) cc_final: 0.8165 (m-30) REVERT: 8 177 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6978 (tppp) REVERT: 8 194 ASP cc_start: 0.8131 (t70) cc_final: 0.7775 (t70) REVERT: 8 205 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8577 (mmmt) REVERT: 8 225 ASP cc_start: 0.7949 (t0) cc_final: 0.7610 (p0) REVERT: C 26 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7527 (ttm-80) REVERT: D 133 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: E 52 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7456 (mtp180) REVERT: E 79 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (mtp85) REVERT: E 81 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8290 (ptt90) REVERT: E 158 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8134 (mtpp) REVERT: F 21 ASP cc_start: 0.8123 (m-30) cc_final: 0.7901 (m-30) REVERT: F 71 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8562 (ttmp) REVERT: F 87 ARG cc_start: 0.8258 (ptt-90) cc_final: 0.7995 (ptt-90) REVERT: G 161 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: J 28 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (tt) REVERT: J 94 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: J 108 MET cc_start: 0.8867 (mtt) cc_final: 0.8605 (mtt) REVERT: K 5 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: K 31 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: M 25 THR cc_start: 0.9031 (p) cc_final: 0.8596 (t) REVERT: M 85 SER cc_start: 0.8626 (t) cc_final: 0.8371 (t) REVERT: N 71 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8077 (mtm-85) REVERT: N 117 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.5840 (mtp85) REVERT: P 93 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8272 (mmt90) REVERT: Q 51 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6754 (mtp180) REVERT: Q 59 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8263 (ttmm) REVERT: R 88 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6818 (mtm180) REVERT: S 30 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (m) REVERT: S 105 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7259 (mtp180) REVERT: T 4 LEU cc_start: 0.7193 (pt) cc_final: 0.6927 (tp) REVERT: U 7 ASP cc_start: 0.7845 (m-30) cc_final: 0.7531 (m-30) REVERT: U 42 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7822 (mtmt) REVERT: V 66 THR cc_start: 0.9210 (m) cc_final: 0.8757 (p) REVERT: V 87 ARG cc_start: 0.8655 (mtm110) cc_final: 0.8347 (mtt90) REVERT: V 99 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6485 (ttm110) REVERT: V 166 VAL cc_start: 0.8867 (t) cc_final: 0.8554 (m) REVERT: X 27 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8707 (ptt90) REVERT: Y 32 LEU cc_start: 0.8965 (mt) cc_final: 0.8755 (mm) REVERT: Z 16 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7746 (mtp-110) REVERT: Z 32 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8522 (mtm180) REVERT: c 17 ASP cc_start: 0.8129 (t70) cc_final: 0.7806 (t70) REVERT: c 57 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7475 (mt-10) REVERT: c 111 GLN cc_start: 0.8625 (tp40) cc_final: 0.8156 (tp40) REVERT: e 60 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7838 (mtp85) REVERT: f 7 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (ttp) REVERT: g 24 THR cc_start: 0.8907 (t) cc_final: 0.8652 (m) REVERT: g 78 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7293 (ttt90) REVERT: g 79 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.6998 (ptm-80) REVERT: g 123 GLU cc_start: 0.8343 (tp30) cc_final: 0.8112 (mm-30) REVERT: g 143 LYS cc_start: 0.8233 (mttp) cc_final: 0.7937 (mtpt) REVERT: g 144 MET cc_start: 0.8453 (tpp) cc_final: 0.8239 (tpt) REVERT: h 43 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7909 (mm-30) REVERT: i 48 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7329 (tttt) REVERT: i 94 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8954 (p) REVERT: i 121 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8682 (tptp) REVERT: i 151 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7122 (ptp-110) REVERT: j 88 MET cc_start: 0.8166 (pmm) cc_final: 0.7925 (pmm) REVERT: k 90 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7633 (mmt-90) REVERT: k 129 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6819 (m110) REVERT: p 72 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7955 (mptm) REVERT: p 84 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8372 (mptm) REVERT: t 22 LYS cc_start: 0.8266 (ttpt) cc_final: 0.8035 (tttm) REVERT: x 12 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.6811 (tmm-80) REVERT: x 23 ASP cc_start: 0.7790 (t70) cc_final: 0.7218 (t70) REVERT: x 56 LYS cc_start: 0.8578 (mptp) cc_final: 0.7974 (mtmt) REVERT: x 93 MET cc_start: 0.7776 (mmm) cc_final: 0.7309 (mpm) REVERT: x 97 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6975 (ptmm) REVERT: x 136 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6938 (t70) REVERT: x 155 GLU cc_start: 0.7552 (mp0) cc_final: 0.6815 (mp0) REVERT: x 230 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: x 400 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7691 (mtpp) REVERT: x 427 SER cc_start: 0.8669 (p) cc_final: 0.8432 (m) outliers start: 164 outliers final: 115 residues processed: 889 average time/residue: 2.1632 time to fit residues: 2795.1113 Evaluate side-chains 937 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 786 time to evaluate : 6.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 GLU Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 21 THR Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 63 VAL Chi-restraints excluded: chain 8 residue 174 VAL Chi-restraints excluded: chain 8 residue 177 LYS Chi-restraints excluded: chain 8 residue 193 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 51 ARG Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 105 ARG Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 99 ARG Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 14 ARG Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 16 ARG Chi-restraints excluded: chain Z residue 32 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 60 ARG Chi-restraints excluded: chain e residue 117 GLN Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 64 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 134 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 42 LEU Chi-restraints excluded: chain i residue 94 SER Chi-restraints excluded: chain i residue 151 ARG Chi-restraints excluded: chain j residue 40 VAL Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 90 LEU Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 72 LYS Chi-restraints excluded: chain p residue 84 LYS Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 115 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain t residue 57 LYS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 70 VAL Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 97 LYS Chi-restraints excluded: chain x residue 136 ASP Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 230 ASP Chi-restraints excluded: chain x residue 555 LEU Chi-restraints excluded: chain x residue 556 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1075 random chunks: chunk 677 optimal weight: 10.0000 chunk 908 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 786 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 854 optimal weight: 0.2980 chunk 357 optimal weight: 8.9990 chunk 877 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 overall best weight: 7.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN L 106 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 ASN ** k 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 HIS ** x 201 HIS ** 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 = 0.3238 r_free = 0.3238 target = 0.103390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.069612 restraints weight = 228137.348| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 1.03 r_work: 0.2546 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 165142 Z= 0.502 Angle : 0.725 18.451 247171 Z= 0.360 Chirality : 0.044 0.377 31514 Planarity : 0.006 0.127 13410 Dihedral : 22.774 179.824 82998 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.13 % Rotamer: Outliers : 3.61 % Allowed : 19.92 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.10), residues: 6072 helix: -0.46 (0.12), residues: 1852 sheet: -0.58 (0.15), residues: 1131 loop : -1.53 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 22 HIS 0.010 0.002 HIS M 13 PHE 0.023 0.002 PHE e 102 TYR 0.022 0.002 TYR C 104 ARG 0.013 0.001 ARG h 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44212.33 seconds wall clock time: 769 minutes 31.50 seconds (46171.50 seconds total)