Starting phenix.real_space_refine on Sun Apr 14 08:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li0_4050/04_2024/5li0_4050_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied External origin is not on a grid point...ignoring external origin ***Please contact the Phenix developers if you need Phenix to use this external_origin*** ------------------------------------------------------------------------------- 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= 0.027 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 1 6.06 5 P 4574 5.49 5 Mg 31 5.21 5 S 120 5.16 5 C 70404 2.51 5 N 25946 2.21 5 O 39749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "S ARG 23": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 39": "NH1" <-> "NH2" Residue "S PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "W ARG 4": "NH1" <-> "NH2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ARG 64": "NH1" <-> "NH2" Residue "X ARG 32": "NH1" <-> "NH2" Residue "X ARG 92": "NH1" <-> "NH2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "0 ARG 17": "NH1" <-> "NH2" Residue "0 ARG 27": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 7": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 58": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "3 GLU 72": "OE1" <-> "OE2" Residue "3 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 35": "NH1" <-> "NH2" Residue "4 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 42": "NH1" <-> "NH2" Residue "5 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 16": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "7 ARG 45": "NH1" <-> "NH2" Residue "7 ARG 48": "NH1" <-> "NH2" Residue "7 ARG 57": "NH1" <-> "NH2" Residue "8 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 140825 Number of models: 1 Model: "" Number of chains: 58 Chain: "a" Number of atoms: 33126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1547, 33126 Classifications: {'RNA': 1547} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 90, 'rna3p_pur': 744, 'rna3p_pyr': 590} Link IDs: {'rna2p': 213, 'rna3p': 1333} Chain: "b" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1802 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1638 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 202} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1600 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 185} Chain breaks: 1 Chain: "e" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1239 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 799 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "g" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1189 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 124} Chain: "i" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 116} Chain: "j" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "k" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 107} Chain: "l" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1063 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "m" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 946 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 6, 'PTRANS': 3, 'TRANS': 109} Chain: "n" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 54} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 590 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 2, 'TRANS': 64} Chain: "s" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'TRANS': 77} Chain: "A" Number of atoms: 62475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2914, 62475 Classifications: {'RNA': 2914} Modifications used: {'rna2p_pur': 293, 'rna2p_pyr': 173, 'rna3p_pur': 1375, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 466, 'rna3p': 2447} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2427 Classifications: {'RNA': 114} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "D" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2104 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 255} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1649 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "F" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1525 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "G" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1312 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1285 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "M" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "O" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 998 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "R" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 113} Chain: "S" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 886 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "T" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "V" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 863 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "W" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 726 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "X" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 669 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 2 Chain: "Y" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "Z" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 627 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 78} Chain: "0" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 374 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "1" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 537 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'TRANS': 64} Chain: "2" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 677 Classifications: {'peptide': 83} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 76} Chain: "4" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 51} Chain: "5" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'CIS': 1, 'TRANS': 26} Chain breaks: 1 Chain: "6" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 488 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'TRANS': 59} Chain: "8" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "a" 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: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Unusual residues: {' O': 9, ' MG': 29} Classifications: {'undetermined': 38} Link IDs: {None: 37} Chain: "8" 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0V6I SG CYS 8 11 109.640 144.654 44.010 1.00 54.96 S ATOM A0V76 SG CYS 8 14 107.388 147.060 45.559 1.00 55.24 S ATOM A0VA0 SG CYS 8 27 106.012 144.630 42.943 1.00 57.50 S Time building chain proxies: 51.34, per 1000 atoms: 0.36 Number of scatterers: 140825 At special positions: 0 Unit cell: (248.6, 269.5, 228.8, 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 1 29.99 S 120 16.00 P 4574 15.00 Mg 31 11.99 O 39749 8.00 N 25946 7.00 C 70404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.12 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " Number of angles added : 3 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9914 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: 143 helices and 58 sheets defined 34.7% alpha, 16.2% beta 1399 base pairs and 2230 stacking pairs defined. Time for finding SS restraints: 66.99 Creating SS restraints... Processing helix chain 'b' and resid 8 through 16 removed outlier: 4.006A pdb=" N VAL b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS b 15 " --> pdb=" O GLU b 11 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE b 16 " --> pdb=" O ALA b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 32 removed outlier: 3.651A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 27 through 32' Processing helix chain 'b' and resid 43 through 64 removed outlier: 3.955A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.811A pdb=" N SER b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 4.068A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER b 108 " --> pdb=" O TYR b 104 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET b 120 " --> pdb=" O GLU b 116 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU b 121 " --> pdb=" O ILE b 117 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP b 123 " --> pdb=" O LYS b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.539A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 removed outlier: 3.690A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 228 removed outlier: 4.755A pdb=" N VAL b 228 " --> pdb=" O GLY b 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.077A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 5.001A pdb=" N LEU c 31 " --> pdb=" O ASP c 27 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.513A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 4.311A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA c 92 " --> pdb=" O ASN c 88 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.755A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.250A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.284A pdb=" N SER d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.629A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.546A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS d 78 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 4.202A pdb=" N ASN d 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.577A pdb=" N LEU d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 4.363A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS d 116 " --> pdb=" O GLN d 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 147 removed outlier: 4.109A pdb=" N GLN d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS d 147 " --> pdb=" O GLU d 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 142 through 147' Processing helix chain 'd' and resid 148 through 157 removed outlier: 4.047A pdb=" N VAL d 152 " --> pdb=" O LEU d 148 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 Proline residue: d 186 - end of helix Processing helix chain 'd' and resid 190 through 200 removed outlier: 4.725A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR d 198 " --> pdb=" O ILE d 194 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.210A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.522A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 Processing helix chain 'e' and resid 149 through 158 removed outlier: 3.929A pdb=" N LYS e 155 " --> pdb=" O GLU e 151 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU e 156 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY e 158 " --> pdb=" O ALA e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 165 removed outlier: 4.483A pdb=" N LEU e 164 " --> pdb=" O THR e 160 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR e 165 " --> pdb=" O VAL e 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 160 through 165' Processing helix chain 'f' and resid 15 through 32 Processing helix chain 'f' and resid 71 through 83 removed outlier: 4.750A pdb=" N GLU f 75 " --> pdb=" O LYS f 71 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE f 82 " --> pdb=" O ARG f 78 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 4.713A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.852A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY g 55 " --> pdb=" O GLU g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.483A pdb=" N MET g 70 " --> pdb=" O ILE g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.732A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 4.320A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 4.627A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 4.189A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.800A pdb=" N LYS h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.741A pdb=" N ALA h 118 " --> pdb=" O THR h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 42 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 46 through 57 removed outlier: 4.054A pdb=" N LEU i 50 " --> pdb=" O LEU i 46 " (cutoff:3.500A) Proline residue: i 53 - end of helix Processing helix chain 'i' and resid 73 through 93 removed outlier: 3.612A pdb=" N GLN i 77 " --> pdb=" O GLY i 73 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS i 83 " --> pdb=" O GLN i 79 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE i 85 " --> pdb=" O ILE i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 104 removed outlier: 4.824A pdb=" N GLY i 98 " --> pdb=" O PRO i 94 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA i 103 " --> pdb=" O SER i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 89 removed outlier: 3.533A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.980A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.038A pdb=" N LYS k 57 " --> pdb=" O LYS k 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 78 removed outlier: 3.898A pdb=" N GLN k 64 " --> pdb=" O PRO k 60 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 104 removed outlier: 4.510A pdb=" N SER k 95 " --> pdb=" O PRO k 91 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA k 103 " --> pdb=" O ALA k 99 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 4.193A pdb=" N LYS l 10 " --> pdb=" O GLN l 6 " (cutoff:3.500A) Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 126 through 131 removed outlier: 4.655A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 15 through 21 removed outlier: 5.710A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 5.222A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN m 31 " --> pdb=" O THR m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 61 removed outlier: 4.835A pdb=" N ARG m 55 " --> pdb=" O ASP m 51 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.084A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.623A pdb=" N ILE m 89 " --> pdb=" O SER m 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG m 93 " --> pdb=" O ILE m 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 110 removed outlier: 5.305A pdb=" N ARG m 109 " --> pdb=" O ASN m 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 12 removed outlier: 4.485A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.596A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY n 51 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.393A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.308A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 5.631A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER o 72 " --> pdb=" O ASN o 68 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP o 74 " --> pdb=" O LEU o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 5.568A pdb=" N ALA p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS p 59 " --> pdb=" O ALA p 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP p 60 " --> pdb=" O LEU p 56 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU p 61 " --> pdb=" O ALA p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.912A pdb=" N ILE p 74 " --> pdb=" O THR p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 80 through 89 Processing helix chain 'r' and resid 30 through 39 removed outlier: 3.872A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS r 35 " --> pdb=" O THR r 31 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG r 36 " --> pdb=" O GLU r 32 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 30 through 39' Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.688A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY r 51 " --> pdb=" O ARG r 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 46 through 51' Processing helix chain 'r' and resid 53 through 71 removed outlier: 3.602A pdb=" N GLN r 57 " --> pdb=" O SER r 53 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR r 62 " --> pdb=" O ARG r 58 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS r 69 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 24 removed outlier: 6.813A pdb=" N MET s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 42 removed outlier: 4.424A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER t 40 " --> pdb=" O LYS t 36 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN t 41 " --> pdb=" O THR t 37 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 61 removed outlier: 5.673A pdb=" N GLU t 48 " --> pdb=" O ASP t 44 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP t 58 " --> pdb=" O VAL t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 5.043A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 removed outlier: 4.036A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 34' Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.276A pdb=" N ILE D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Proline residue: D 135 - end of helix No H-bonds generated for 'chain 'D' and resid 130 through 135' Processing helix chain 'D' and resid 206 through 214 removed outlier: 4.002A pdb=" N SER D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 4.660A pdb=" N MET D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 225' Processing helix chain 'D' and resid 265 through 270 removed outlier: 5.278A pdb=" N VAL D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 81 removed outlier: 4.265A pdb=" N LYS E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA E 80 " --> pdb=" O HIS E 76 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'F' and resid 29 through 46 removed outlier: 4.142A pdb=" N ARG F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 121 removed outlier: 3.720A pdb=" N ARG F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 4.127A pdb=" N GLU F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN F 141 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 163 removed outlier: 5.100A pdb=" N ASP F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 156 through 163' Processing helix chain 'F' and resid 177 through 183 removed outlier: 4.276A pdb=" N VAL F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 removed outlier: 4.358A pdb=" N THR F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 removed outlier: 3.665A pdb=" N ILE F 26 " --> pdb=" O ASP F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 21 through 26' Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.720A pdb=" N ASN G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 11 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 4.120A pdb=" N VAL G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix No H-bonds generated for 'chain 'G' and resid 24 through 29' Processing helix chain 'G' and resid 45 through 59 removed outlier: 4.574A pdb=" N VAL G 49 " --> pdb=" O GLN G 45 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 99 removed outlier: 3.817A pdb=" N GLY G 93 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR G 97 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 166 removed outlier: 4.069A pdb=" N THR G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 81 removed outlier: 3.613A pdb=" N THR H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 153 removed outlier: 4.723A pdb=" N VAL H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Proline residue: H 153 - end of helix Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.614A pdb=" N LEU M 29 " --> pdb=" O THR M 25 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 97 removed outlier: 4.765A pdb=" N ARG M 95 " --> pdb=" O GLY M 91 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN M 97 " --> pdb=" O LEU M 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 91 through 97' Processing helix chain 'M' and resid 98 through 111 removed outlier: 4.318A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Proline residue: M 111 - end of helix Processing helix chain 'M' and resid 113 through 123 removed outlier: 3.798A pdb=" N LYS M 121 " --> pdb=" O GLU M 117 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.835A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY N 109 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 removed outlier: 4.858A pdb=" N VAL N 115 " --> pdb=" O PHE N 111 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU N 117 " --> pdb=" O LYS N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 126 removed outlier: 3.714A pdb=" N LYS O 124 " --> pdb=" O LYS O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 removed outlier: 3.769A pdb=" N ILE P 47 " --> pdb=" O THR P 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET P 58 " --> pdb=" O MET P 54 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 removed outlier: 4.236A pdb=" N ALA P 114 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS P 124 " --> pdb=" O LEU P 120 " (cutoff:3.500A) Proline residue: P 126 - end of helix Processing helix chain 'Q' and resid 9 through 28 removed outlier: 3.698A pdb=" N LEU Q 24 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE Q 26 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER Q 27 " --> pdb=" O SER Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 54 removed outlier: 3.740A pdb=" N LYS Q 52 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS Q 53 " --> pdb=" O THR Q 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 66 removed outlier: 4.895A pdb=" N LYS Q 64 " --> pdb=" O ARG Q 60 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR Q 65 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 94 removed outlier: 6.130A pdb=" N LYS Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA Q 90 " --> pdb=" O PHE Q 86 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU Q 91 " --> pdb=" O GLY Q 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG Q 92 " --> pdb=" O GLU Q 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR Q 93 " --> pdb=" O ILE Q 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 4.292A pdb=" N VAL R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG R 19 " --> pdb=" O HIS R 15 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 88 removed outlier: 3.854A pdb=" N ALA R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP R 86 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS R 87 " --> pdb=" O LYS R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 116 removed outlier: 6.299A pdb=" N ALA R 107 " --> pdb=" O GLY R 103 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 63 removed outlier: 4.159A pdb=" N ILE R 63 " --> pdb=" O SER R 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 58 through 63' Processing helix chain 'S' and resid 4 through 16 removed outlier: 6.528A pdb=" N GLU S 8 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA S 9 " --> pdb=" O LYS S 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER S 13 " --> pdb=" O ALA S 9 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU S 15 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 22 removed outlier: 6.940A pdb=" N ARG T 11 " --> pdb=" O GLY T 7 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA T 21 " --> pdb=" O THR T 17 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS T 22 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 72 removed outlier: 4.865A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 removed outlier: 3.592A pdb=" N LEU T 79 " --> pdb=" O SER T 75 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 102 removed outlier: 4.673A pdb=" N LEU T 95 " --> pdb=" O ASN T 91 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 117 removed outlier: 4.414A pdb=" N ALA T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 25 removed outlier: 3.999A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE V 24 " --> pdb=" O VAL V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 40 removed outlier: 3.572A pdb=" N THR V 39 " --> pdb=" O ILE V 35 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 61 Proline residue: V 45 - end of helix Processing helix chain 'W' and resid 2 through 8 removed outlier: 4.467A pdb=" N LYS W 8 " --> pdb=" O ARG W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 23 removed outlier: 4.171A pdb=" N ALA W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP W 23 " --> pdb=" O ALA W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 46 removed outlier: 3.980A pdb=" N VAL W 38 " --> pdb=" O ASN W 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 25 removed outlier: 4.427A pdb=" N LEU Y 21 " --> pdb=" O ASP Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 55 removed outlier: 3.530A pdb=" N PHE Y 48 " --> pdb=" O ASP Y 44 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG Y 53 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) Processing helix chain '0' and resid 50 through 55 removed outlier: 4.384A pdb=" N LEU 0 54 " --> pdb=" O SER 0 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS 0 55 " --> pdb=" O ALA 0 51 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 50 through 55' Processing helix chain '1' and resid 2 through 9 removed outlier: 5.916A pdb=" N ILE 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 9' Processing helix chain '1' and resid 10 through 35 removed outlier: 6.823A pdb=" N ILE 1 14 " --> pdb=" O THR 1 10 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU 1 16 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR 1 34 " --> pdb=" O PHE 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 66 removed outlier: 4.077A pdb=" N THR 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 4.019A pdb=" N LEU 2 26 " --> pdb=" O THR 2 22 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.508A pdb=" N ARG 2 44 " --> pdb=" O ASN 2 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL 2 50 " --> pdb=" O GLN 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 56 removed outlier: 7.602A pdb=" N HIS 3 55 " --> pdb=" O SER 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix No H-bonds generated for 'chain '3' and resid 51 through 56' Processing helix chain '3' and resid 68 through 83 Processing helix chain '4' and resid 9 through 19 removed outlier: 3.875A pdb=" N ASN 4 14 " --> pdb=" O LYS 4 10 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG 4 17 " --> pdb=" O LYS 4 13 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR 4 18 " --> pdb=" O ASN 4 14 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 16 removed outlier: 4.317A pdb=" N HIS 6 13 " --> pdb=" O ASN 6 9 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 6 16 " --> pdb=" O LYS 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 26 removed outlier: 3.756A pdb=" N ARG 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS 6 26 " --> pdb=" O ARG 6 22 " (cutoff:3.500A) Processing helix chain '6' and resid 27 through 39 removed outlier: 3.975A pdb=" N GLY 6 39 " --> pdb=" O ARG 6 35 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 14 removed outlier: 4.922A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL 7 14 " --> pdb=" O ALA 7 10 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 9 through 14' Processing helix chain '7' and resid 34 through 40 removed outlier: 5.162A pdb=" N GLN 7 40 " --> pdb=" O LYS 7 36 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 53 removed outlier: 4.657A pdb=" N SER 7 51 " --> pdb=" O ALA 7 47 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS 7 52 " --> pdb=" O ARG 7 48 " (cutoff:3.500A) Processing helix chain '8' and resid 29 through 34 removed outlier: 3.942A pdb=" N LYS 8 33 " --> pdb=" O ASN 8 29 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN 8 34 " --> pdb=" O PRO 8 30 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 29 through 34' Processing sheet with id= 1, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.890A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL b 70 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL b 163 " --> pdb=" O VAL b 184 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 19 through 22 removed outlier: 5.637A pdb=" N GLU c 19 " --> pdb=" O VAL c 54 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA c 66 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE c 65 " --> pdb=" O HIS c 99 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR c 69 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 166 through 170 removed outlier: 4.518A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN c 151 " --> pdb=" O LYS c 198 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS c 198 " --> pdb=" O GLN c 151 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL c 197 " --> pdb=" O ALA c 186 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP c 182 " --> pdb=" O ILE c 201 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 165 through 169 removed outlier: 3.755A pdb=" N THR d 175 " --> pdb=" O ASN d 166 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 11 through 16 removed outlier: 4.235A pdb=" N GLY e 40 " --> pdb=" O GLU e 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL e 16 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL e 21 " --> pdb=" O ARG e 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN e 19 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU e 36 " --> pdb=" O THR e 17 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 83 through 89 removed outlier: 8.101A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE e 85 " --> pdb=" O MET e 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR e 89 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE e 123 " --> pdb=" O GLY e 104 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 33 through 41 removed outlier: 6.635A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.899A pdb=" N GLU f 39 " --> pdb=" O ARG f 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE f 62 " --> pdb=" O LYS f 41 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP f 43 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 44 through 47 Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 78 removed outlier: 6.840A pdb=" N VAL g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL g 91 " --> pdb=" O VAL g 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 27 removed outlier: 6.290A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU h 27 " --> pdb=" O LEU h 60 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 76 through 80 removed outlier: 3.716A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE h 128 " --> pdb=" O ILE h 80 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 7 through 13 Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.524A pdb=" N LEU j 42 " --> pdb=" O LYS j 71 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA j 12 " --> pdb=" O HIS j 70 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG j 72 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG j 9 " --> pdb=" O GLU j 99 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 29 through 36 removed outlier: 4.227A pdb=" N ASN k 29 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY k 19 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE k 23 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS k 87 " --> pdb=" O ILE k 23 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER k 25 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY k 88 " --> pdb=" O VAL k 113 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 42 through 47 Processing sheet with id= 17, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.834A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.571A pdb=" N LEU p 10 " --> pdb=" O PHE p 17 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR p 18 " --> pdb=" O TYR p 40 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE p 20 " --> pdb=" O GLY p 38 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS p 51 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 8 through 13 removed outlier: 6.367A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU q 65 " --> pdb=" O LYS q 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR q 10 " --> pdb=" O ILE q 63 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 30 through 33 removed outlier: 4.021A pdb=" N ALA s 50 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.629A pdb=" N VAL D 115 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 113 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.185A pdb=" N SER D 79 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 90 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 138 through 141 removed outlier: 4.307A pdb=" N THR D 138 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 140 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 169 through 175 removed outlier: 8.218A pdb=" N LYS D 169 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER D 185 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.160A pdb=" N LYS E 3 " --> pdb=" O THR E 213 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 5 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG E 212 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 118 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 180 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASN E 176 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 11 through 17 removed outlier: 4.215A pdb=" N GLY E 11 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN E 187 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.874A pdb=" N GLN E 50 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN E 33 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL E 105 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN E 103 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.534A pdb=" N ARG E 89 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE E 87 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 114 through 117 removed outlier: 4.777A pdb=" N ASP E 114 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.646A pdb=" N ASP F 5 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER F 16 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU F 7 " --> pdb=" O SER F 14 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 167 through 171 removed outlier: 4.358A pdb=" N GLN F 148 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 82 through 87 removed outlier: 4.419A pdb=" N MET G 83 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET G 38 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE G 85 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL G 36 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA G 87 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS G 33 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 35 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN G 37 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY G 39 " --> pdb=" O TYR G 143 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR G 143 " --> pdb=" O GLY G 39 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'H' and resid 15 through 19 removed outlier: 3.629A pdb=" N THR H 16 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'H' and resid 41 through 45 removed outlier: 4.302A pdb=" N THR H 42 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 53 " --> pdb=" O THR H 42 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 51 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H' and resid 82 through 89 removed outlier: 3.501A pdb=" N VAL H 133 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU H 87 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL H 131 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR H 129 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 122 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 94 through 98 removed outlier: 3.607A pdb=" N ILE H 115 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 105 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 113 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 15 through 20 Processing sheet with id= 39, first strand: chain 'N' and resid 17 through 21 removed outlier: 7.093A pdb=" N ARG N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL N 10 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU N 8 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR N 6 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN N 82 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS N 9 " --> pdb=" O ASN N 82 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA N 11 " --> pdb=" O CYS N 84 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 38 through 41 Processing sheet with id= 41, first strand: chain 'O' and resid 66 through 70 removed outlier: 4.547A pdb=" N LEU O 96 " --> pdb=" O THR O 67 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 63 through 66 removed outlier: 3.826A pdb=" N GLU P 105 " --> pdb=" O TRP P 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS P 128 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 29 through 33 removed outlier: 3.999A pdb=" N ALA Q 114 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'R' and resid 50 through 53 removed outlier: 6.083A pdb=" N ILE R 44 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR R 41 " --> pdb=" O TYR R 34 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR R 34 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN R 43 " --> pdb=" O ASN R 32 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL R 33 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'R' and resid 41 through 44 removed outlier: 3.775A pdb=" N ALA R 42 " --> pdb=" O ALA R 56 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 51 through 54 removed outlier: 3.641A pdb=" N LYS S 51 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR S 62 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR S 62 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 36 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY S 47 " --> pdb=" O LEU S 28 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP S 26 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR S 27 " --> pdb=" O LYS S 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS S 89 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 59 through 67 removed outlier: 8.416A pdb=" N GLU S 59 " --> pdb=" O LEU S 78 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE S 76 " --> pdb=" O PHE S 61 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'U' and resid 18 through 23 removed outlier: 5.096A pdb=" N GLN U 18 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS U 94 " --> pdb=" O ASN U 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR U 96 " --> pdb=" O THR U 61 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR U 59 " --> pdb=" O ASP U 98 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'U' and resid 70 through 76 removed outlier: 4.049A pdb=" N ILE U 71 " --> pdb=" O HIS U 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS U 88 " --> pdb=" O ILE U 71 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL U 73 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS U 86 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 1 through 8 removed outlier: 5.662A pdb=" N MET V 1 " --> pdb=" O ASP V 109 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP V 109 " --> pdb=" O MET V 1 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 24 through 28 removed outlier: 3.903A pdb=" N ARG W 75 " --> pdb=" O TYR W 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS W 77 " --> pdb=" O MET W 56 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR W 81 " --> pdb=" O SER W 52 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER W 52 " --> pdb=" O THR W 81 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 25 through 28 removed outlier: 4.867A pdb=" N ALA X 25 " --> pdb=" O VAL X 34 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU X 27 " --> pdb=" O ARG X 32 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG X 32 " --> pdb=" O LEU X 27 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Y' and resid 38 through 43 removed outlier: 4.253A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 91 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Y' and resid 60 through 64 removed outlier: 3.508A pdb=" N ILE Y 70 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Z' and resid 59 through 62 removed outlier: 3.716A pdb=" N GLY Z 60 " --> pdb=" O PHE Z 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY Z 62 " --> pdb=" O THR Z 66 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR Z 66 " --> pdb=" O GLY Z 62 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Z' and resid 73 through 79 removed outlier: 3.507A pdb=" N LYS Z 76 " --> pdb=" O SER Z 88 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain '2' and resid 34 through 38 removed outlier: 4.000A pdb=" N VAL 2 35 " --> pdb=" O ILE 2 6 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN 2 5 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR 2 7 " --> pdb=" O THR 2 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR 2 9 " --> pdb=" O LEU 2 53 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU 2 53 " --> pdb=" O THR 2 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain '8' and resid 14 through 19 removed outlier: 3.582A pdb=" N ILE 8 17 " --> pdb=" O MET 8 24 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS 8 22 " --> pdb=" O ARG 8 19 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3490 hydrogen bonds 5694 hydrogen bond angles 0 basepair planarities 1399 basepair parallelities 2230 stacking parallelities Total time for adding SS restraints: 241.75 Time building geometry restraints manager: 67.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.48: 96364 1.48 - 1.75: 56334 1.75 - 2.03: 217 2.03 - 2.31: 8 2.31 - 2.59: 7 Bond restraints: 152930 Sorted by residual: bond pdb=" C1' G A2230 " pdb=" N9 G A2230 " ideal model delta sigma weight residual 1.475 2.437 -0.962 1.50e-02 4.44e+03 4.11e+03 bond pdb=" C6 G A1288 " pdb=" N1 G A1288 " ideal model delta sigma weight residual 1.391 2.589 -1.198 2.00e-02 2.50e+03 3.59e+03 bond pdb=" C5 C A 857 " pdb=" C6 C A 857 " ideal model delta sigma weight residual 1.339 2.457 -1.118 2.00e-02 2.50e+03 3.12e+03 bond pdb=" N1 G A1288 " pdb=" C2 G A1288 " ideal model delta sigma weight residual 1.373 2.482 -1.109 2.00e-02 2.50e+03 3.07e+03 bond pdb=" N3 G A1288 " pdb=" C4 G A1288 " ideal model delta sigma weight residual 1.350 2.385 -1.035 2.00e-02 2.50e+03 2.68e+03 ... (remaining 152925 not shown) Histogram of bond angle deviations from ideal: 26.62 - 53.70: 2 53.70 - 80.79: 1 80.79 - 107.87: 41414 107.87 - 134.95: 187593 134.95 - 162.03: 19 Bond angle restraints: 229029 Sorted by residual: angle pdb=" N3 C A 857 " pdb=" C4 C A 857 " pdb=" C5 C A 857 " ideal model delta sigma weight residual 121.90 26.62 95.28 3.00e+00 1.11e-01 1.01e+03 angle pdb=" C2 C A 857 " pdb=" N1 C A 857 " pdb=" C6 C A 857 " ideal model delta sigma weight residual 120.20 29.37 90.83 3.00e+00 1.11e-01 9.17e+02 angle pdb=" C2' G A2230 " pdb=" C1' G A2230 " pdb=" N9 G A2230 " ideal model delta sigma weight residual 112.00 136.51 -24.51 1.50e+00 4.44e-01 2.67e+02 angle pdb=" C2 C A 857 " pdb=" N3 C A 857 " pdb=" C4 C A 857 " ideal model delta sigma weight residual 119.90 161.67 -41.77 3.00e+00 1.11e-01 1.94e+02 angle pdb=" N1 C A 857 " pdb=" C6 C A 857 " pdb=" C5 C A 857 " ideal model delta sigma weight residual 121.00 162.03 -41.03 3.00e+00 1.11e-01 1.87e+02 ... (remaining 229024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 86837 35.86 - 71.72: 9862 71.72 - 107.57: 1031 107.57 - 143.43: 21 143.43 - 179.29: 16 Dihedral angle restraints: 97767 sinusoidal: 82368 harmonic: 15399 Sorted by residual: dihedral pdb=" CA ALA c 24 " pdb=" C ALA c 24 " pdb=" N GLU c 25 " pdb=" CA GLU c 25 " ideal model delta harmonic sigma weight residual 180.00 68.24 111.76 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA LYS m 64 " pdb=" C LYS m 64 " pdb=" N VAL m 65 " pdb=" CA VAL m 65 " ideal model delta harmonic sigma weight residual 180.00 71.53 108.47 0 5.00e+00 4.00e-02 4.71e+02 dihedral pdb=" CA LEU h 98 " pdb=" C LEU h 98 " pdb=" N ASN h 99 " pdb=" CA ASN h 99 " ideal model delta harmonic sigma weight residual -180.00 -123.21 -56.79 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 97764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 27545 0.101 - 0.202: 1702 0.202 - 0.304: 74 0.304 - 0.405: 8 0.405 - 0.506: 2 Chirality restraints: 29331 Sorted by residual: chirality pdb=" C1' C A 785 " pdb=" O4' C A 785 " pdb=" C2' C A 785 " pdb=" N1 C A 785 " both_signs ideal model delta sigma weight residual False 2.47 1.96 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" C1' U A2022 " pdb=" O4' U A2022 " pdb=" C2' U A2022 " pdb=" N1 U A2022 " both_signs ideal model delta sigma weight residual False 2.47 2.04 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ASP s 65 " pdb=" N ASP s 65 " pdb=" C ASP s 65 " pdb=" CB ASP s 65 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 29328 not shown) Planarity restraints: 12042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 857 " -0.062 2.00e-02 2.50e+03 5.27e-02 6.26e+01 pdb=" N1 C A 857 " 0.100 2.00e-02 2.50e+03 pdb=" C2 C A 857 " -0.043 2.00e-02 2.50e+03 pdb=" O2 C A 857 " 0.028 2.00e-02 2.50e+03 pdb=" N3 C A 857 " 0.059 2.00e-02 2.50e+03 pdb=" C4 C A 857 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 857 " -0.036 2.00e-02 2.50e+03 pdb=" C5 C A 857 " 0.015 2.00e-02 2.50e+03 pdb=" C6 C A 857 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU g 13 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO g 14 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO g 14 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO g 14 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A1801 " -0.043 2.00e-02 2.50e+03 3.55e-02 2.83e+01 pdb=" N1 C A1801 " 0.055 2.00e-02 2.50e+03 pdb=" C2 C A1801 " -0.022 2.00e-02 2.50e+03 pdb=" O2 C A1801 " -0.010 2.00e-02 2.50e+03 pdb=" N3 C A1801 " 0.061 2.00e-02 2.50e+03 pdb=" C4 C A1801 " -0.038 2.00e-02 2.50e+03 pdb=" N4 C A1801 " -0.022 2.00e-02 2.50e+03 pdb=" C5 C A1801 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A1801 " 0.016 2.00e-02 2.50e+03 ... (remaining 12039 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 1240 2.52 - 3.11: 104644 3.11 - 3.71: 263784 3.71 - 4.30: 358321 4.30 - 4.90: 512462 Nonbonded interactions: 1240451 Sorted by model distance: nonbonded pdb=" O2' U a 420 " pdb=" O4' G a 421 " model vdw 1.920 2.440 nonbonded pdb=" OP1 A A2475 " pdb="MG MG A3002 " model vdw 1.927 2.170 nonbonded pdb=" O4' U A1971 " pdb=" O2' U A1982 " model vdw 1.933 2.440 nonbonded pdb=" N3 C A 857 " pdb=" C6 C A 857 " model vdw 1.938 2.736 nonbonded pdb=" N3 C A 857 " pdb=" N1 G A1288 " model vdw 1.960 2.600 ... (remaining 1240446 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.140 Extract box with map and model: 12.250 Check model and map are aligned: 1.390 Set scattering table: 0.860 Process input model: 543.910 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.420 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: 0.040 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 566.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.014 1.198 152930 Z= 0.827 Angle : 1.177 95.278 229029 Z= 0.573 Chirality : 0.054 0.506 29331 Planarity : 0.007 0.145 12042 Dihedral : 22.547 179.290 87853 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 14.87 % Favored : 84.67 % Rotamer: Outliers : 0.20 % Allowed : 0.85 % Favored : 98.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.89 % Twisted Proline : 2.72 % Twisted General : 1.20 % 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: -5.64 (0.09), residues: 5292 helix: -3.49 (0.09), residues: 1414 sheet: -4.14 (0.13), residues: 806 loop : -3.91 (0.09), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP F 83 HIS 0.016 0.004 HIS 7 31 PHE 0.031 0.004 PHE G 99 TYR 0.041 0.004 TYR P 74 ARG 0.026 0.002 ARG m 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1828 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1819 time to evaluate : 5.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 83 GLU cc_start: 0.5623 (mm-30) cc_final: 0.5236 (mm-30) REVERT: b 96 TRP cc_start: 0.7838 (t-100) cc_final: 0.7466 (t-100) REVERT: b 199 VAL cc_start: 0.7638 (t) cc_final: 0.7421 (m) REVERT: b 223 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7395 (tp30) REVERT: c 26 LYS cc_start: 0.6282 (pttm) cc_final: 0.6058 (ptpt) REVERT: c 48 GLU cc_start: 0.7713 (pt0) cc_final: 0.7504 (pt0) REVERT: c 53 HIS cc_start: 0.7961 (p-80) cc_final: 0.6928 (p-80) REVERT: c 104 GLU cc_start: 0.5216 (tp30) cc_final: 0.4853 (tm-30) REVERT: d 184 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6289 (tt0) REVERT: e 14 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6189 (ttm-80) REVERT: e 117 LEU cc_start: 0.8834 (tp) cc_final: 0.8262 (tp) REVERT: g 33 ASP cc_start: 0.6423 (m-30) cc_final: 0.5583 (t0) REVERT: g 115 THR cc_start: 0.7750 (m) cc_final: 0.7493 (m) REVERT: g 136 LYS cc_start: 0.8449 (mttp) cc_final: 0.8044 (mttm) REVERT: g 137 LYS cc_start: 0.7933 (tptm) cc_final: 0.7227 (tmtt) REVERT: h 25 LEU cc_start: 0.8420 (tp) cc_final: 0.7943 (tp) REVERT: h 31 ASN cc_start: 0.7575 (p0) cc_final: 0.7325 (p0) REVERT: h 64 LEU cc_start: 0.9062 (mp) cc_final: 0.8784 (mt) REVERT: h 119 ARG cc_start: 0.7220 (ptp90) cc_final: 0.6535 (ttp-110) REVERT: i 107 THR cc_start: 0.7957 (p) cc_final: 0.7601 (t) REVERT: j 49 TYR cc_start: 0.7018 (m-80) cc_final: 0.6744 (m-80) REVERT: j 57 MET cc_start: 0.6977 (ptm) cc_final: 0.6668 (ptm) REVERT: k 61 PHE cc_start: 0.6404 (t80) cc_final: 0.5173 (t80) REVERT: m 68 ASP cc_start: 0.7299 (m-30) cc_final: 0.6989 (p0) REVERT: m 77 ILE cc_start: 0.7782 (pt) cc_final: 0.7559 (pt) REVERT: n 47 LEU cc_start: 0.8356 (mt) cc_final: 0.8145 (mt) REVERT: p 77 LYS cc_start: 0.6586 (mttt) cc_final: 0.6354 (mtmt) REVERT: q 35 LEU cc_start: 0.8419 (tp) cc_final: 0.8191 (mm) REVERT: q 48 THR cc_start: 0.8502 (m) cc_final: 0.8083 (p) REVERT: s 6 LYS cc_start: 0.5857 (mttt) cc_final: 0.5294 (pttt) REVERT: s 37 ARG cc_start: 0.4958 (mtt-85) cc_final: 0.4396 (mtm180) REVERT: t 21 ASN cc_start: 0.8158 (m-40) cc_final: 0.7929 (m-40) REVERT: E 79 LYS cc_start: 0.6674 (tttm) cc_final: 0.6343 (ttmm) REVERT: F 186 ILE cc_start: 0.4837 (mm) cc_final: 0.4480 (mm) REVERT: G 27 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6177 (mt-10) REVERT: H 10 ASP cc_start: 0.6018 (t0) cc_final: 0.5634 (m-30) REVERT: H 115 ILE cc_start: 0.7118 (mt) cc_final: 0.6797 (tt) REVERT: M 125 VAL cc_start: 0.9390 (t) cc_final: 0.8951 (m) REVERT: Q 112 ASP cc_start: 0.8364 (p0) cc_final: 0.7747 (p0) REVERT: R 101 TYR cc_start: 0.7614 (t80) cc_final: 0.7207 (t80) REVERT: T 96 SER cc_start: 0.7856 (m) cc_final: 0.7621 (t) REVERT: T 100 ILE cc_start: 0.8370 (mt) cc_final: 0.8168 (mt) REVERT: U 32 THR cc_start: 0.6540 (p) cc_final: 0.6176 (p) REVERT: U 36 ASP cc_start: 0.7636 (m-30) cc_final: 0.7048 (m-30) REVERT: U 92 TYR cc_start: 0.8227 (p90) cc_final: 0.7888 (p90) REVERT: V 8 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7202 (mmt180) REVERT: V 86 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7958 (mmm160) REVERT: W 61 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8513 (mtpt) REVERT: W 74 LYS cc_start: 0.8625 (tttt) cc_final: 0.7726 (tttm) REVERT: X 29 LYS cc_start: 0.8339 (mttm) cc_final: 0.7378 (mtmm) REVERT: X 77 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7151 (pm20) REVERT: Y 42 LYS cc_start: 0.8791 (mttp) cc_final: 0.8533 (mttm) REVERT: Y 53 ARG cc_start: 0.6766 (mtm180) cc_final: 0.6552 (mmt180) REVERT: Z 54 TYR cc_start: 0.8131 (m-80) cc_final: 0.7871 (m-80) REVERT: 0 10 ARG cc_start: 0.5785 (mtm180) cc_final: 0.4993 (ttp-110) REVERT: 3 78 PHE cc_start: 0.4889 (p90) cc_final: 0.4659 (p90) REVERT: 3 81 LYS cc_start: 0.4176 (OUTLIER) cc_final: 0.3480 (mttt) REVERT: 4 10 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8072 (ptpp) REVERT: 5 17 TYR cc_start: 0.5791 (m-80) cc_final: 0.5552 (m-80) outliers start: 9 outliers final: 3 residues processed: 1828 average time/residue: 1.4951 time to fit residues: 4563.9718 Evaluate side-chains 1129 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1125 time to evaluate : 5.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 73 ARG Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 3 residue 81 LYS Chi-restraints excluded: chain 3 residue 83 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 821 optimal weight: 9.9990 chunk 737 optimal weight: 9.9990 chunk 409 optimal weight: 30.0000 chunk 251 optimal weight: 7.9990 chunk 497 optimal weight: 5.9990 chunk 394 optimal weight: 20.0000 chunk 762 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 463 optimal weight: 5.9990 chunk 567 optimal weight: 20.0000 chunk 883 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 8 GLN ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN c 122 GLN ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN e 135 ASN g 106 ASN i 16 ASN i 33 ASN i 77 GLN i 128 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 67 GLN l 73 ASN m 76 ASN m 91 HIS o 68 ASN q 49 HIS s 43 ASN ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN D 113 GLN D 203 ASN E 66 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS E 136 GLN E 167 GLN E 182 ASN F 38 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN H 147 ASN M 80 ASN M 119 GLN N 13 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 4 HIS S 43 GLN T 108 GLN U 81 ASN V 102 HIS X 69 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Z 86 GLN 1 31 GLN 3 10 HIS 4 51 ASN 6 7 GLN 6 13 HIS ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.730 152930 Z= 0.429 Angle : 0.862 90.597 229029 Z= 0.416 Chirality : 0.041 0.711 29331 Planarity : 0.006 0.132 12042 Dihedral : 23.273 178.777 76887 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.36 % Favored : 88.40 % Rotamer: Outliers : 3.85 % Allowed : 12.78 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.47 % 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: -4.27 (0.10), residues: 5292 helix: -1.79 (0.12), residues: 1464 sheet: -3.30 (0.15), residues: 832 loop : -3.36 (0.09), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP P 41 HIS 0.013 0.002 HIS o 51 PHE 0.028 0.003 PHE p 84 TYR 0.030 0.003 TYR r 56 ARG 0.014 0.001 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1328 time to evaluate : 5.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 21 ARG cc_start: 0.3871 (mmt180) cc_final: 0.3598 (mmt180) REVERT: b 56 PHE cc_start: 0.8268 (t80) cc_final: 0.8001 (t80) REVERT: b 103 ASN cc_start: 0.7463 (t0) cc_final: 0.7256 (t0) REVERT: b 199 VAL cc_start: 0.7806 (t) cc_final: 0.7501 (m) REVERT: c 41 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: c 99 HIS cc_start: 0.7921 (t-170) cc_final: 0.7534 (t-170) REVERT: c 101 ASN cc_start: 0.7692 (m-40) cc_final: 0.7456 (m-40) REVERT: c 135 GLN cc_start: 0.6744 (pt0) cc_final: 0.6054 (mp10) REVERT: c 146 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: c 163 ARG cc_start: 0.7530 (ttp-110) cc_final: 0.7070 (tpm170) REVERT: d 8 ASN cc_start: 0.6456 (m110) cc_final: 0.6153 (m110) REVERT: d 51 LEU cc_start: 0.7775 (tp) cc_final: 0.7368 (tp) REVERT: d 55 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: d 150 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5595 (mp) REVERT: f 22 LEU cc_start: 0.7798 (tp) cc_final: 0.7570 (tt) REVERT: f 75 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: g 74 GLU cc_start: 0.6456 (tt0) cc_final: 0.6214 (tt0) REVERT: g 136 LYS cc_start: 0.8539 (mttp) cc_final: 0.8285 (mttp) REVERT: h 26 GLU cc_start: 0.7602 (mp0) cc_final: 0.7220 (mp0) REVERT: h 27 LEU cc_start: 0.6287 (tp) cc_final: 0.5285 (tp) REVERT: h 119 ARG cc_start: 0.7622 (ptp90) cc_final: 0.7155 (ttp-110) REVERT: i 54 PHE cc_start: 0.7318 (m-80) cc_final: 0.7041 (m-80) REVERT: i 58 GLU cc_start: 0.5773 (tt0) cc_final: 0.5442 (tm-30) REVERT: i 85 ILE cc_start: 0.8545 (mt) cc_final: 0.8254 (mm) REVERT: i 101 LYS cc_start: 0.7059 (mmmt) cc_final: 0.6459 (mmmt) REVERT: j 49 TYR cc_start: 0.7167 (m-80) cc_final: 0.6658 (m-80) REVERT: j 57 MET cc_start: 0.7056 (ptm) cc_final: 0.6671 (ptm) REVERT: j 58 TYR cc_start: 0.6824 (m-80) cc_final: 0.6426 (m-80) REVERT: j 67 GLN cc_start: 0.8174 (tt0) cc_final: 0.7960 (tt0) REVERT: l 47 CYS cc_start: 0.8485 (m) cc_final: 0.8112 (m) REVERT: l 56 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.7108 (mtm-85) REVERT: l 103 LEU cc_start: 0.7971 (mp) cc_final: 0.7667 (mp) REVERT: m 3 ARG cc_start: 0.7272 (tpp80) cc_final: 0.7035 (mmm-85) REVERT: m 81 MET cc_start: 0.7177 (tmm) cc_final: 0.6718 (mtp) REVERT: m 107 ARG cc_start: 0.6632 (mtm180) cc_final: 0.6405 (mtp180) REVERT: n 10 GLN cc_start: 0.5605 (mm-40) cc_final: 0.5150 (mm-40) REVERT: p 15 ASN cc_start: 0.8740 (m-40) cc_final: 0.8353 (m-40) REVERT: p 39 THR cc_start: 0.8238 (t) cc_final: 0.7945 (m) REVERT: q 10 TYR cc_start: 0.8185 (m-10) cc_final: 0.7801 (m-10) REVERT: q 26 LEU cc_start: 0.9136 (tp) cc_final: 0.8912 (tt) REVERT: q 35 LEU cc_start: 0.8557 (tp) cc_final: 0.8105 (mm) REVERT: s 6 LYS cc_start: 0.5580 (mttt) cc_final: 0.5215 (pttt) REVERT: s 37 ARG cc_start: 0.5042 (mtt-85) cc_final: 0.4474 (mtm180) REVERT: s 48 THR cc_start: 0.7642 (m) cc_final: 0.7309 (p) REVERT: D 202 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9201 (m) REVERT: D 275 LYS cc_start: 0.6849 (ptpt) cc_final: 0.6336 (ptpt) REVERT: F 79 ARG cc_start: 0.9027 (mpt-90) cc_final: 0.8796 (mpt-90) REVERT: G 27 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6182 (mt-10) REVERT: M 45 TYR cc_start: 0.8435 (t80) cc_final: 0.8016 (t80) REVERT: N 31 LYS cc_start: 0.8177 (pttm) cc_final: 0.7973 (mttm) REVERT: P 51 ARG cc_start: 0.6817 (tmt170) cc_final: 0.6581 (tpt90) REVERT: P 112 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7076 (tm-30) REVERT: Q 112 ASP cc_start: 0.8537 (p0) cc_final: 0.8179 (p0) REVERT: R 92 ILE cc_start: 0.7351 (pp) cc_final: 0.7101 (pp) REVERT: R 102 HIS cc_start: 0.5807 (p-80) cc_final: 0.5468 (t-170) REVERT: T 74 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7775 (tmm) REVERT: U 32 THR cc_start: 0.6729 (p) cc_final: 0.6402 (p) REVERT: U 78 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8600 (ptt90) REVERT: U 92 TYR cc_start: 0.8296 (p90) cc_final: 0.7852 (p90) REVERT: W 26 THR cc_start: 0.9041 (t) cc_final: 0.8759 (p) REVERT: X 29 LYS cc_start: 0.8312 (mttm) cc_final: 0.7730 (mtmm) REVERT: X 31 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: Y 85 GLN cc_start: 0.8008 (pt0) cc_final: 0.7723 (pm20) REVERT: 0 10 ARG cc_start: 0.5641 (mtm180) cc_final: 0.5039 (ttp-110) REVERT: 1 15 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6704 (pt0) REVERT: 1 16 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7658 (mm-30) REVERT: 3 77 LYS cc_start: 0.4379 (OUTLIER) cc_final: 0.3818 (mmmt) REVERT: 4 10 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8623 (ptpp) REVERT: 7 55 MET cc_start: 0.7213 (tmm) cc_final: 0.6658 (tmm) outliers start: 176 outliers final: 97 residues processed: 1404 average time/residue: 1.3674 time to fit residues: 3306.7543 Evaluate side-chains 1180 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1072 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 27 ASP Chi-restraints excluded: chain c residue 41 PHE Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 79 PHE Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 78 ARG Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 0 residue 18 ARG Chi-restraints excluded: chain 1 residue 15 GLU Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 73 ARG Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 6 residue 7 GLN Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 491 optimal weight: 50.0000 chunk 274 optimal weight: 0.9980 chunk 735 optimal weight: 0.7980 chunk 601 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 885 optimal weight: 7.9990 chunk 956 optimal weight: 3.9990 chunk 788 optimal weight: 5.9990 chunk 877 optimal weight: 20.0000 chunk 301 optimal weight: 0.0670 chunk 710 optimal weight: 8.9990 overall best weight: 2.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 190 ASN c 3 GLN ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 43 ASN i 33 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 ASN k 22 HIS ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 HIS P 13 HIS P 123 HIS ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS S 43 GLN ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.711 152930 Z= 0.350 Angle : 0.708 84.883 229029 Z= 0.342 Chirality : 0.035 0.708 29331 Planarity : 0.005 0.120 12042 Dihedral : 23.083 178.726 76883 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.16 % Favored : 90.65 % Rotamer: Outliers : 3.19 % Allowed : 17.26 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.27 % 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: -3.39 (0.10), residues: 5292 helix: -0.94 (0.12), residues: 1487 sheet: -2.64 (0.16), residues: 878 loop : -2.93 (0.10), residues: 2927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP b 23 HIS 0.009 0.001 HIS c 175 PHE 0.028 0.002 PHE O 128 TYR 0.036 0.002 TYR 4 37 ARG 0.034 0.001 ARG q 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1282 time to evaluate : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 35 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7691 (ttp80) REVERT: b 114 ILE cc_start: 0.5876 (mt) cc_final: 0.5535 (mt) REVERT: b 199 VAL cc_start: 0.7828 (t) cc_final: 0.7531 (m) REVERT: b 207 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6924 (mt) REVERT: c 41 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: c 69 THR cc_start: 0.5579 (t) cc_final: 0.5179 (m) REVERT: c 99 HIS cc_start: 0.7952 (t-170) cc_final: 0.7616 (t-170) REVERT: c 135 GLN cc_start: 0.6917 (pt0) cc_final: 0.6180 (mp10) REVERT: c 163 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7043 (tpm170) REVERT: d 8 ASN cc_start: 0.6034 (m110) cc_final: 0.5727 (m110) REVERT: d 55 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: d 99 TYR cc_start: 0.7694 (t80) cc_final: 0.7441 (t80) REVERT: d 146 GLN cc_start: 0.7978 (pp30) cc_final: 0.7453 (pp30) REVERT: f 65 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.6994 (p) REVERT: f 66 LYS cc_start: 0.7886 (tmmt) cc_final: 0.7634 (tmmt) REVERT: f 67 SER cc_start: 0.9098 (p) cc_final: 0.8870 (t) REVERT: f 88 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7353 (mtp85) REVERT: g 96 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7274 (ttp-170) REVERT: g 136 LYS cc_start: 0.8533 (mttp) cc_final: 0.8253 (mttp) REVERT: g 137 LYS cc_start: 0.8336 (tptm) cc_final: 0.7593 (tttm) REVERT: g 149 LYS cc_start: 0.7363 (pttm) cc_final: 0.6869 (pttm) REVERT: h 23 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6636 (tp30) REVERT: h 60 LEU cc_start: 0.8550 (tp) cc_final: 0.8306 (tt) REVERT: h 70 ASP cc_start: 0.6985 (t0) cc_final: 0.6525 (t0) REVERT: h 94 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6901 (pmm) REVERT: h 119 ARG cc_start: 0.7543 (ptp90) cc_final: 0.7102 (ttp-110) REVERT: i 39 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6226 (tp30) REVERT: i 85 ILE cc_start: 0.8376 (mt) cc_final: 0.8109 (mm) REVERT: i 101 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6690 (mmmt) REVERT: j 49 TYR cc_start: 0.6909 (m-80) cc_final: 0.6602 (m-80) REVERT: j 57 MET cc_start: 0.6676 (ptm) cc_final: 0.6401 (ptm) REVERT: j 58 TYR cc_start: 0.6448 (m-80) cc_final: 0.6236 (m-80) REVERT: k 61 PHE cc_start: 0.6937 (t80) cc_final: 0.6542 (t80) REVERT: k 82 VAL cc_start: 0.6356 (p) cc_final: 0.6124 (p) REVERT: l 47 CYS cc_start: 0.8241 (m) cc_final: 0.7945 (m) REVERT: l 72 ASN cc_start: 0.7979 (p0) cc_final: 0.7685 (p0) REVERT: m 68 ASP cc_start: 0.6588 (p0) cc_final: 0.5287 (p0) REVERT: m 81 MET cc_start: 0.6668 (tmm) cc_final: 0.6385 (ptp) REVERT: n 10 GLN cc_start: 0.5575 (mm-40) cc_final: 0.5084 (mm-40) REVERT: p 15 ASN cc_start: 0.8713 (m-40) cc_final: 0.8327 (m110) REVERT: p 39 THR cc_start: 0.8078 (t) cc_final: 0.7762 (m) REVERT: q 10 TYR cc_start: 0.8190 (m-10) cc_final: 0.7952 (m-10) REVERT: q 35 LEU cc_start: 0.8626 (tp) cc_final: 0.8199 (mm) REVERT: s 37 ARG cc_start: 0.5241 (mtt-85) cc_final: 0.4655 (mtm180) REVERT: t 50 VAL cc_start: 0.9093 (m) cc_final: 0.8837 (p) REVERT: F 101 MET cc_start: 0.6857 (mmm) cc_final: 0.6253 (mmm) REVERT: G 27 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6217 (mt-10) REVERT: M 38 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6989 (tmm160) REVERT: N 120 GLU cc_start: 0.7348 (pm20) cc_final: 0.6943 (pt0) REVERT: O 98 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7716 (mt-10) REVERT: Q 45 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6743 (mt-10) REVERT: Q 112 ASP cc_start: 0.8708 (p0) cc_final: 0.8396 (p0) REVERT: R 101 TYR cc_start: 0.6986 (t80) cc_final: 0.6465 (t80) REVERT: R 102 HIS cc_start: 0.6079 (p-80) cc_final: 0.5792 (t-170) REVERT: T 59 LYS cc_start: 0.8643 (mttt) cc_final: 0.8381 (mtpt) REVERT: T 74 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7440 (tmm) REVERT: U 23 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: U 92 TYR cc_start: 0.8128 (p90) cc_final: 0.7702 (p90) REVERT: V 64 MET cc_start: 0.6016 (mtt) cc_final: 0.5742 (mtm) REVERT: W 26 THR cc_start: 0.8955 (t) cc_final: 0.8744 (p) REVERT: X 29 LYS cc_start: 0.8306 (mttm) cc_final: 0.7728 (mtmm) REVERT: X 31 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: Y 73 MET cc_start: 0.6401 (ptm) cc_final: 0.6198 (ttp) REVERT: 2 18 THR cc_start: 0.7837 (p) cc_final: 0.7633 (m) REVERT: 4 10 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8580 (ptpp) REVERT: 5 19 THR cc_start: 0.6258 (OUTLIER) cc_final: 0.6047 (p) REVERT: 7 55 MET cc_start: 0.7197 (tmm) cc_final: 0.6776 (tmm) outliers start: 146 outliers final: 76 residues processed: 1349 average time/residue: 1.3333 time to fit residues: 3127.8403 Evaluate side-chains 1175 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1089 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 41 PHE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain e residue 136 MET Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain o residue 84 SER Chi-restraints excluded: chain q residue 25 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 6 residue 24 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 874 optimal weight: 10.0000 chunk 665 optimal weight: 20.0000 chunk 459 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 422 optimal weight: 20.0000 chunk 594 optimal weight: 50.0000 chunk 888 optimal weight: 9.9990 chunk 940 optimal weight: 20.0000 chunk 464 optimal weight: 10.0000 chunk 841 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 ASN b 190 ASN c 125 ASN ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN e 146 ASN g 40 GLN i 128 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN r 57 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 74 ASN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN E 192 ASN F 75 GLN H 81 GLN H 147 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 HIS W 34 ASN ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN X 67 ASN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 17 GLN 1 36 GLN 4 14 ASN 6 7 GLN ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.721 152930 Z= 0.470 Angle : 0.855 84.154 229029 Z= 0.412 Chirality : 0.042 0.692 29331 Planarity : 0.006 0.129 12042 Dihedral : 23.094 178.957 76875 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.02 % Favored : 87.72 % Rotamer: Outliers : 5.99 % Allowed : 18.97 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.31 % 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: -3.32 (0.10), residues: 5292 helix: -0.79 (0.12), residues: 1471 sheet: -2.67 (0.16), residues: 877 loop : -2.91 (0.10), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP b 23 HIS 0.014 0.002 HIS o 51 PHE 0.028 0.003 PHE G 114 TYR 0.032 0.003 TYR W 68 ARG 0.052 0.001 ARG c 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1156 time to evaluate : 5.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.3919 (OUTLIER) cc_final: 0.3596 (ppp) REVERT: b 41 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5578 (mm) REVERT: b 199 VAL cc_start: 0.7969 (t) cc_final: 0.7694 (m) REVERT: b 216 LYS cc_start: 0.7119 (pttm) cc_final: 0.6865 (pttm) REVERT: c 135 GLN cc_start: 0.7061 (pt0) cc_final: 0.6589 (mm-40) REVERT: c 163 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6771 (tpm170) REVERT: c 180 ASP cc_start: 0.6678 (m-30) cc_final: 0.6214 (m-30) REVERT: d 8 ASN cc_start: 0.6535 (m110) cc_final: 0.6235 (m110) REVERT: d 55 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: d 68 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: e 11 PHE cc_start: 0.5468 (m-10) cc_final: 0.5256 (m-80) REVERT: e 14 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7154 (mtm110) REVERT: e 20 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7558 (ptm160) REVERT: f 65 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7075 (p) REVERT: f 88 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7713 (mtp85) REVERT: g 149 LYS cc_start: 0.7722 (pttm) cc_final: 0.7401 (pttm) REVERT: h 16 ASN cc_start: 0.8758 (m-40) cc_final: 0.8548 (m110) REVERT: h 23 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6688 (tp30) REVERT: h 70 ASP cc_start: 0.7536 (t0) cc_final: 0.7215 (t0) REVERT: h 94 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7190 (pmm) REVERT: h 119 ARG cc_start: 0.7857 (ptp90) cc_final: 0.7289 (ttp-110) REVERT: i 85 ILE cc_start: 0.8598 (mt) cc_final: 0.8310 (mm) REVERT: i 101 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6784 (mmmt) REVERT: j 9 ARG cc_start: 0.7345 (ttm170) cc_final: 0.6550 (ttm170) REVERT: j 49 TYR cc_start: 0.7090 (m-80) cc_final: 0.6824 (m-80) REVERT: j 57 MET cc_start: 0.7114 (ptm) cc_final: 0.6805 (ptm) REVERT: j 58 TYR cc_start: 0.6801 (m-80) cc_final: 0.6478 (m-80) REVERT: k 29 ASN cc_start: 0.7048 (t0) cc_final: 0.6819 (m-40) REVERT: l 7 LEU cc_start: 0.9342 (mt) cc_final: 0.8926 (mt) REVERT: l 72 ASN cc_start: 0.8154 (p0) cc_final: 0.7835 (p0) REVERT: m 69 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7021 (tt) REVERT: n 10 GLN cc_start: 0.5556 (mm-40) cc_final: 0.5156 (mm-40) REVERT: p 15 ASN cc_start: 0.8877 (m-40) cc_final: 0.8467 (m110) REVERT: s 37 ARG cc_start: 0.5172 (mtt-85) cc_final: 0.4769 (mtm-85) REVERT: t 74 ILE cc_start: 0.8869 (tp) cc_final: 0.8402 (mt) REVERT: D 275 LYS cc_start: 0.6803 (ptpt) cc_final: 0.6541 (ptpt) REVERT: M 32 GLU cc_start: 0.7004 (pt0) cc_final: 0.6601 (pt0) REVERT: M 38 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7278 (tmm160) REVERT: M 54 TYR cc_start: 0.8151 (m-80) cc_final: 0.7815 (m-80) REVERT: Q 52 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8373 (mtmm) REVERT: Q 112 ASP cc_start: 0.8578 (p0) cc_final: 0.8054 (p0) REVERT: Q 120 GLU cc_start: 0.8504 (pm20) cc_final: 0.8250 (pm20) REVERT: R 101 TYR cc_start: 0.7852 (t80) cc_final: 0.7609 (t80) REVERT: R 102 HIS cc_start: 0.6108 (p-80) cc_final: 0.5894 (t-170) REVERT: U 23 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: U 78 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8342 (ptt90) REVERT: U 92 TYR cc_start: 0.8410 (p90) cc_final: 0.8108 (p90) REVERT: V 15 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7337 (mtp85) REVERT: V 40 ASN cc_start: 0.7102 (p0) cc_final: 0.6485 (p0) REVERT: W 26 THR cc_start: 0.8998 (t) cc_final: 0.8784 (p) REVERT: W 58 TYR cc_start: 0.8196 (m-80) cc_final: 0.7981 (m-80) REVERT: Z 54 TYR cc_start: 0.8289 (m-80) cc_final: 0.8041 (m-80) REVERT: 1 16 GLU cc_start: 0.7448 (tp30) cc_final: 0.7215 (tp30) REVERT: 1 30 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7607 (t80) REVERT: 4 8 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8947 (p) REVERT: 4 10 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8634 (mttt) REVERT: 6 12 LYS cc_start: 0.8797 (mttt) cc_final: 0.8315 (mtpt) REVERT: 7 53 SER cc_start: 0.8655 (p) cc_final: 0.8411 (p) outliers start: 274 outliers final: 183 residues processed: 1289 average time/residue: 1.2083 time to fit residues: 2694.5758 Evaluate side-chains 1261 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1065 time to evaluate : 5.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 68 PHE Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 79 PHE Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 31 THR Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain m residue 31 GLN Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 78 ARG Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 48 ASN Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 6 residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 783 optimal weight: 10.0000 chunk 533 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 700 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 802 optimal weight: 1.9990 chunk 650 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 844 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 overall best weight: 5.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN c 175 HIS ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 ASN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 GLN t 21 ASN t 62 GLN ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN F 75 GLN H 64 ASN H 81 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN X 67 ASN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN 6 7 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.717 152930 Z= 0.392 Angle : 0.745 84.446 229029 Z= 0.361 Chirality : 0.037 0.708 29331 Planarity : 0.005 0.125 12042 Dihedral : 23.045 179.247 76873 Min Nonbonded Distance : 1.343 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.29 % Rotamer: Outliers : 5.71 % Allowed : 21.70 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.27 % 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: -3.02 (0.11), residues: 5292 helix: -0.49 (0.13), residues: 1486 sheet: -2.44 (0.16), residues: 894 loop : -2.77 (0.10), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 41 HIS 0.012 0.001 HIS o 51 PHE 0.025 0.002 PHE 6 19 TYR 0.023 0.002 TYR W 68 ARG 0.015 0.001 ARG 4 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1144 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.4027 (OUTLIER) cc_final: 0.3402 (ppp) REVERT: b 41 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5512 (mm) REVERT: b 199 VAL cc_start: 0.7924 (t) cc_final: 0.7657 (m) REVERT: b 207 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6925 (mt) REVERT: c 47 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6310 (mtmt) REVERT: c 135 GLN cc_start: 0.7018 (pt0) cc_final: 0.6569 (mp10) REVERT: c 163 ARG cc_start: 0.7164 (ttp-110) cc_final: 0.6767 (tpm170) REVERT: c 180 ASP cc_start: 0.6531 (m-30) cc_final: 0.6272 (m-30) REVERT: d 8 ASN cc_start: 0.6456 (m110) cc_final: 0.6137 (m110) REVERT: e 20 ARG cc_start: 0.8152 (ptm160) cc_final: 0.7556 (ptm160) REVERT: f 65 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7173 (p) REVERT: f 88 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7487 (mtp85) REVERT: g 137 LYS cc_start: 0.8412 (tptm) cc_final: 0.7693 (tttt) REVERT: h 23 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6641 (tp30) REVERT: h 60 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8429 (tt) REVERT: h 70 ASP cc_start: 0.7008 (t0) cc_final: 0.6464 (t0) REVERT: h 94 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7210 (pmm) REVERT: i 101 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6838 (mmmt) REVERT: j 31 ARG cc_start: 0.6605 (mmm160) cc_final: 0.6399 (mmm160) REVERT: j 58 TYR cc_start: 0.6593 (m-80) cc_final: 0.6346 (m-80) REVERT: j 73 LEU cc_start: 0.8755 (mt) cc_final: 0.8430 (mt) REVERT: l 35 PHE cc_start: 0.2155 (OUTLIER) cc_final: 0.0540 (m-80) REVERT: m 69 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (tt) REVERT: n 10 GLN cc_start: 0.5647 (mm-40) cc_final: 0.5259 (mm-40) REVERT: n 34 TYR cc_start: 0.8226 (m-80) cc_final: 0.7772 (m-80) REVERT: p 15 ASN cc_start: 0.8832 (m-40) cc_final: 0.8449 (m110) REVERT: s 34 TRP cc_start: 0.4832 (p90) cc_final: 0.4332 (p90) REVERT: s 37 ARG cc_start: 0.5520 (mtt-85) cc_final: 0.4832 (mtm-85) REVERT: t 34 ASN cc_start: 0.8025 (t0) cc_final: 0.7464 (t0) REVERT: t 49 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8076 (mt) REVERT: D 32 LEU cc_start: 0.9023 (mp) cc_final: 0.8665 (mt) REVERT: D 275 LYS cc_start: 0.6722 (ptpt) cc_final: 0.6378 (ptpt) REVERT: E 134 HIS cc_start: 0.8471 (m170) cc_final: 0.8150 (m170) REVERT: E 141 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7444 (mmt) REVERT: M 38 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7324 (tmm160) REVERT: Q 52 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8342 (mtmm) REVERT: Q 112 ASP cc_start: 0.8708 (p0) cc_final: 0.8163 (p0) REVERT: Q 120 GLU cc_start: 0.8435 (pm20) cc_final: 0.8220 (pm20) REVERT: R 101 TYR cc_start: 0.7632 (t80) cc_final: 0.7328 (t80) REVERT: T 55 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6913 (ttm110) REVERT: T 74 MET cc_start: 0.8138 (mmm) cc_final: 0.7805 (tmm) REVERT: U 23 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: U 92 TYR cc_start: 0.8335 (p90) cc_final: 0.7991 (p90) REVERT: V 40 ASN cc_start: 0.7089 (p0) cc_final: 0.6561 (p0) REVERT: W 26 THR cc_start: 0.8981 (t) cc_final: 0.8776 (p) REVERT: X 31 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: 1 16 GLU cc_start: 0.7340 (tp30) cc_final: 0.7040 (tp30) REVERT: 1 30 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7584 (t80) REVERT: 2 6 ILE cc_start: 0.8675 (mm) cc_final: 0.8331 (mm) REVERT: 4 8 THR cc_start: 0.9193 (m) cc_final: 0.8947 (p) REVERT: 4 10 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8673 (mttt) REVERT: 6 12 LYS cc_start: 0.8804 (mttt) cc_final: 0.8281 (mtpt) REVERT: 7 55 MET cc_start: 0.7330 (tmm) cc_final: 0.6966 (tmm) outliers start: 261 outliers final: 181 residues processed: 1261 average time/residue: 1.2114 time to fit residues: 2645.1640 Evaluate side-chains 1254 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1058 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 40 GLN Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 31 THR Chi-restraints excluded: chain i residue 36 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain r residue 69 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 48 ASN Chi-restraints excluded: chain 3 residue 28 THR Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 7 residue 14 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 316 optimal weight: 5.9990 chunk 846 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 552 optimal weight: 20.0000 chunk 232 optimal weight: 7.9990 chunk 941 optimal weight: 5.9990 chunk 781 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 494 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN c 3 GLN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 ASN h 16 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 67 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN n 52 GLN t 21 ASN ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN ** 5 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.719 152930 Z= 0.413 Angle : 0.769 84.220 229029 Z= 0.372 Chirality : 0.038 0.701 29331 Planarity : 0.005 0.125 12042 Dihedral : 23.038 179.097 76873 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.62 % Favored : 88.15 % Rotamer: Outliers : 6.41 % Allowed : 21.59 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.99 % Twisted Proline : 1.09 % Twisted General : 0.29 % 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: -2.93 (0.11), residues: 5292 helix: -0.41 (0.13), residues: 1481 sheet: -2.35 (0.16), residues: 899 loop : -2.72 (0.10), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP 3 37 HIS 0.038 0.002 HIS c 175 PHE 0.031 0.002 PHE G 114 TYR 0.028 0.002 TYR W 68 ARG 0.011 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1113 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 41 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5621 (mm) REVERT: b 68 LEU cc_start: 0.8602 (mt) cc_final: 0.8369 (mt) REVERT: b 199 VAL cc_start: 0.8016 (t) cc_final: 0.7748 (m) REVERT: b 207 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.6902 (mt) REVERT: b 216 LYS cc_start: 0.7161 (pttt) cc_final: 0.6567 (pttm) REVERT: c 47 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6386 (mtmt) REVERT: c 117 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6943 (tm-30) REVERT: c 135 GLN cc_start: 0.6919 (pt0) cc_final: 0.6677 (mp10) REVERT: c 175 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7310 (t-90) REVERT: c 180 ASP cc_start: 0.6559 (m-30) cc_final: 0.6323 (m-30) REVERT: d 8 ASN cc_start: 0.6569 (m110) cc_final: 0.6248 (m110) REVERT: f 65 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7230 (p) REVERT: g 149 LYS cc_start: 0.7613 (pttm) cc_final: 0.7407 (pttm) REVERT: h 16 ASN cc_start: 0.8870 (m-40) cc_final: 0.8627 (m110) REVERT: h 23 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6660 (tp30) REVERT: h 24 LYS cc_start: 0.8840 (ptmm) cc_final: 0.8505 (ptpp) REVERT: h 70 ASP cc_start: 0.7020 (t0) cc_final: 0.6479 (t0) REVERT: h 94 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7208 (pmm) REVERT: i 101 LYS cc_start: 0.7080 (mmmt) cc_final: 0.6775 (mmmt) REVERT: j 58 TYR cc_start: 0.6755 (m-80) cc_final: 0.6449 (m-80) REVERT: j 73 LEU cc_start: 0.8785 (mt) cc_final: 0.8441 (mt) REVERT: l 35 PHE cc_start: 0.2141 (OUTLIER) cc_final: 0.0460 (m-80) REVERT: l 85 HIS cc_start: 0.6989 (p-80) cc_final: 0.6713 (p-80) REVERT: m 69 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (tt) REVERT: n 10 GLN cc_start: 0.5637 (mm-40) cc_final: 0.5142 (mm-40) REVERT: n 34 TYR cc_start: 0.8135 (m-80) cc_final: 0.7816 (m-80) REVERT: n 50 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7492 (mtmm) REVERT: n 52 GLN cc_start: 0.6640 (mt0) cc_final: 0.6365 (mt0) REVERT: p 15 ASN cc_start: 0.8846 (m-40) cc_final: 0.8453 (m-40) REVERT: q 76 ARG cc_start: 0.6624 (mtt180) cc_final: 0.5547 (mtm180) REVERT: t 34 ASN cc_start: 0.8038 (t0) cc_final: 0.7595 (t0) REVERT: t 39 VAL cc_start: 0.7569 (t) cc_final: 0.7324 (t) REVERT: t 74 ILE cc_start: 0.8886 (tp) cc_final: 0.8412 (mt) REVERT: t 78 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8380 (tt) REVERT: D 32 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 275 LYS cc_start: 0.6778 (ptpt) cc_final: 0.6464 (ptpt) REVERT: E 122 SER cc_start: 0.9500 (t) cc_final: 0.9114 (m) REVERT: M 38 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7276 (tmm160) REVERT: N 13 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7105 (p0) REVERT: P 37 THR cc_start: 0.8901 (p) cc_final: 0.8290 (t) REVERT: Q 52 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8430 (mtmm) REVERT: Q 112 ASP cc_start: 0.8709 (p0) cc_final: 0.8219 (p0) REVERT: R 101 TYR cc_start: 0.7433 (t80) cc_final: 0.7080 (t80) REVERT: T 55 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6933 (ttm110) REVERT: T 74 MET cc_start: 0.8198 (mmm) cc_final: 0.7938 (tmm) REVERT: U 23 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: U 78 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: V 15 ARG cc_start: 0.7552 (mtp180) cc_final: 0.7340 (mtp85) REVERT: V 40 ASN cc_start: 0.7088 (p0) cc_final: 0.6581 (p0) REVERT: X 31 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: 1 16 GLU cc_start: 0.7576 (tp30) cc_final: 0.7274 (tp30) REVERT: 1 30 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7590 (t80) REVERT: 4 8 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8939 (p) REVERT: 4 10 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8527 (mttt) REVERT: 6 12 LYS cc_start: 0.8818 (mttt) cc_final: 0.8343 (mtpt) REVERT: 7 55 MET cc_start: 0.7293 (tmm) cc_final: 0.6866 (tmm) outliers start: 293 outliers final: 228 residues processed: 1258 average time/residue: 1.2169 time to fit residues: 2654.5581 Evaluate side-chains 1307 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1062 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 175 HIS Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 8 THR Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 146 ASN Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 40 GLN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 31 THR Chi-restraints excluded: chain i residue 36 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 31 GLN Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 84 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 87 ILE Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain r residue 69 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 50 ASP Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 78 ARG Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 38 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 47 ILE Chi-restraints excluded: chain 3 residue 14 PHE Chi-restraints excluded: chain 3 residue 28 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 5 residue 44 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 53 SER Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 907 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 536 optimal weight: 30.0000 chunk 687 optimal weight: 6.9990 chunk 532 optimal weight: 30.0000 chunk 792 optimal weight: 0.0040 chunk 525 optimal weight: 20.0000 chunk 937 optimal weight: 0.3980 chunk 586 optimal weight: 10.0000 chunk 571 optimal weight: 20.0000 chunk 432 optimal weight: 10.0000 overall best weight: 5.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN F 75 GLN H 74 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN U 101 ASN X 67 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN ** 5 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.716 152930 Z= 0.385 Angle : 0.729 84.443 229029 Z= 0.353 Chirality : 0.036 0.716 29331 Planarity : 0.005 0.127 12042 Dihedral : 23.019 178.379 76873 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.85 % Favored : 88.98 % Rotamer: Outliers : 5.97 % Allowed : 23.06 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.99 % Twisted Proline : 1.09 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.11), residues: 5292 helix: -0.28 (0.13), residues: 1480 sheet: -2.15 (0.16), residues: 888 loop : -2.64 (0.10), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 41 HIS 0.016 0.002 HIS b 18 PHE 0.029 0.002 PHE 3 78 TYR 0.028 0.002 TYR n 16 ARG 0.011 0.001 ARG 4 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1126 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 41 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5863 (mm) REVERT: b 199 VAL cc_start: 0.7984 (t) cc_final: 0.7734 (m) REVERT: b 207 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6912 (mt) REVERT: b 216 LYS cc_start: 0.6905 (pttt) cc_final: 0.6512 (pttm) REVERT: c 47 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6324 (mtmt) REVERT: c 69 THR cc_start: 0.6351 (t) cc_final: 0.5959 (m) REVERT: c 163 ARG cc_start: 0.7522 (ttp-110) cc_final: 0.7133 (tpm170) REVERT: c 180 ASP cc_start: 0.6513 (m-30) cc_final: 0.6293 (m-30) REVERT: c 200 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.6617 (m100) REVERT: d 8 ASN cc_start: 0.6527 (m110) cc_final: 0.6231 (m110) REVERT: e 14 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7627 (mtp-110) REVERT: e 52 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8136 (ptpt) REVERT: f 65 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7284 (p) REVERT: g 95 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8002 (tpt170) REVERT: h 16 ASN cc_start: 0.8847 (m-40) cc_final: 0.8613 (m110) REVERT: h 23 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6621 (tp30) REVERT: h 24 LYS cc_start: 0.8817 (ptmm) cc_final: 0.8497 (ptpp) REVERT: h 70 ASP cc_start: 0.6838 (t0) cc_final: 0.6319 (t0) REVERT: h 94 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7208 (pmm) REVERT: i 101 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6616 (mmmt) REVERT: j 23 GLU cc_start: 0.6814 (pm20) cc_final: 0.6524 (pm20) REVERT: j 58 TYR cc_start: 0.6632 (m-80) cc_final: 0.6376 (m-80) REVERT: j 64 GLN cc_start: 0.8246 (pp30) cc_final: 0.7692 (pp30) REVERT: j 73 LEU cc_start: 0.8753 (mt) cc_final: 0.8423 (mt) REVERT: k 98 ARG cc_start: 0.6939 (ttm110) cc_final: 0.6457 (ptp90) REVERT: l 35 PHE cc_start: 0.2046 (OUTLIER) cc_final: 0.0382 (m-80) REVERT: l 85 HIS cc_start: 0.6942 (p-80) cc_final: 0.6670 (p-80) REVERT: m 42 ASP cc_start: 0.3759 (t70) cc_final: 0.3000 (t0) REVERT: m 69 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7160 (tt) REVERT: n 10 GLN cc_start: 0.5482 (mm-40) cc_final: 0.4859 (mm110) REVERT: n 34 TYR cc_start: 0.7989 (m-80) cc_final: 0.7749 (m-80) REVERT: p 15 ASN cc_start: 0.8791 (m-40) cc_final: 0.8411 (m-40) REVERT: s 34 TRP cc_start: 0.4514 (p90) cc_final: 0.4049 (p90) REVERT: t 39 VAL cc_start: 0.7430 (t) cc_final: 0.7226 (t) REVERT: D 32 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8572 (mt) REVERT: E 122 SER cc_start: 0.9508 (t) cc_final: 0.9139 (m) REVERT: E 198 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8013 (tttt) REVERT: E 217 LYS cc_start: 0.7397 (ptpt) cc_final: 0.6980 (mtmt) REVERT: M 38 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7387 (tmm160) REVERT: N 13 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7252 (p0) REVERT: P 37 THR cc_start: 0.8891 (p) cc_final: 0.8262 (t) REVERT: Q 45 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7039 (mt-10) REVERT: Q 52 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8430 (mtmm) REVERT: Q 112 ASP cc_start: 0.8797 (p0) cc_final: 0.8277 (p0) REVERT: S 50 ILE cc_start: 0.9018 (mm) cc_final: 0.8708 (mt) REVERT: T 55 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6924 (ttm110) REVERT: T 74 MET cc_start: 0.8142 (mmm) cc_final: 0.7890 (tmm) REVERT: U 23 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: V 40 ASN cc_start: 0.7160 (p0) cc_final: 0.6776 (p0) REVERT: X 31 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: 1 16 GLU cc_start: 0.7415 (tp30) cc_final: 0.7045 (tp30) REVERT: 1 30 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7527 (t80) REVERT: 1 43 ILE cc_start: 0.8862 (mm) cc_final: 0.8660 (mm) REVERT: 4 8 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8942 (p) REVERT: 4 10 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8425 (mttt) REVERT: 6 12 LYS cc_start: 0.8809 (mttt) cc_final: 0.8340 (mtpt) REVERT: 7 55 MET cc_start: 0.7349 (tmm) cc_final: 0.6982 (tmm) outliers start: 273 outliers final: 221 residues processed: 1254 average time/residue: 1.2433 time to fit residues: 2700.6710 Evaluate side-chains 1319 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1079 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 40 GLN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 31 THR Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 87 ILE Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain r residue 69 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 38 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 2 residue 48 ASN Chi-restraints excluded: chain 3 residue 14 PHE Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 70 ARG Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 580 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 560 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 596 optimal weight: 50.0000 chunk 638 optimal weight: 10.0000 chunk 463 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 737 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 GLN t 21 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.715 152930 Z= 0.371 Angle : 0.709 84.458 229029 Z= 0.342 Chirality : 0.035 0.722 29331 Planarity : 0.005 0.127 12042 Dihedral : 22.985 178.221 76873 Min Nonbonded Distance : 1.343 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.92 % Favored : 88.91 % Rotamer: Outliers : 5.84 % Allowed : 23.78 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.11), residues: 5292 helix: -0.17 (0.13), residues: 1478 sheet: -1.99 (0.17), residues: 867 loop : -2.59 (0.10), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 41 HIS 0.016 0.001 HIS 5 45 PHE 0.029 0.002 PHE 3 78 TYR 0.028 0.002 TYR n 16 ARG 0.008 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1123 time to evaluate : 5.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 41 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.6044 (mm) REVERT: b 199 VAL cc_start: 0.7968 (t) cc_final: 0.7707 (m) REVERT: b 207 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6944 (mt) REVERT: c 47 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6290 (mtmt) REVERT: c 163 ARG cc_start: 0.7345 (ttp-110) cc_final: 0.7101 (tpm170) REVERT: d 8 ASN cc_start: 0.6515 (m110) cc_final: 0.6216 (m110) REVERT: e 14 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7402 (mtm-85) REVERT: e 52 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8116 (ptpt) REVERT: f 65 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7368 (p) REVERT: g 73 LEU cc_start: 0.7973 (mm) cc_final: 0.7388 (tt) REVERT: g 95 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7972 (tpt170) REVERT: h 16 ASN cc_start: 0.8748 (m-40) cc_final: 0.8539 (m110) REVERT: h 24 LYS cc_start: 0.8807 (ptmm) cc_final: 0.8593 (ptpp) REVERT: h 70 ASP cc_start: 0.6844 (t0) cc_final: 0.6259 (t0) REVERT: h 94 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7274 (pmm) REVERT: i 101 LYS cc_start: 0.7007 (mmmt) cc_final: 0.6614 (mmmt) REVERT: i 118 PRO cc_start: 0.5100 (Cg_exo) cc_final: 0.4894 (Cg_endo) REVERT: j 23 GLU cc_start: 0.7109 (pm20) cc_final: 0.6829 (pm20) REVERT: j 58 TYR cc_start: 0.6771 (m-80) cc_final: 0.6556 (m-80) REVERT: j 64 GLN cc_start: 0.8143 (pp30) cc_final: 0.7538 (pp30) REVERT: j 73 LEU cc_start: 0.8758 (mt) cc_final: 0.8417 (mt) REVERT: k 98 ARG cc_start: 0.6898 (ttm110) cc_final: 0.6499 (ptp90) REVERT: l 35 PHE cc_start: 0.2006 (OUTLIER) cc_final: 0.0482 (m-80) REVERT: m 42 ASP cc_start: 0.3630 (t70) cc_final: 0.3052 (t0) REVERT: m 69 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7148 (tt) REVERT: n 34 TYR cc_start: 0.7976 (m-80) cc_final: 0.7739 (m-80) REVERT: p 15 ASN cc_start: 0.8803 (m-40) cc_final: 0.8415 (m-40) REVERT: q 65 GLU cc_start: 0.7873 (pm20) cc_final: 0.7575 (tm-30) REVERT: t 39 VAL cc_start: 0.7271 (t) cc_final: 0.7069 (t) REVERT: D 32 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8743 (mp) REVERT: D 42 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8529 (ptp-170) REVERT: E 122 SER cc_start: 0.9476 (t) cc_final: 0.9175 (m) REVERT: E 198 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8099 (tttt) REVERT: F 35 GLU cc_start: 0.7066 (pp20) cc_final: 0.6817 (pp20) REVERT: M 38 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7394 (tmm160) REVERT: N 13 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7279 (p0) REVERT: Q 45 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6981 (mt-10) REVERT: Q 52 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8420 (mtmm) REVERT: Q 112 ASP cc_start: 0.8822 (p0) cc_final: 0.8249 (p0) REVERT: Q 120 GLU cc_start: 0.8465 (pm20) cc_final: 0.8150 (pm20) REVERT: S 50 ILE cc_start: 0.9035 (mm) cc_final: 0.8730 (mt) REVERT: U 23 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: U 78 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8269 (ptt90) REVERT: V 40 ASN cc_start: 0.7208 (p0) cc_final: 0.6833 (p0) REVERT: X 31 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: 1 16 GLU cc_start: 0.7461 (tp30) cc_final: 0.7102 (tp30) REVERT: 1 30 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7436 (t80) REVERT: 1 43 ILE cc_start: 0.8861 (mm) cc_final: 0.8644 (mm) REVERT: 1 50 ILE cc_start: 0.9386 (mt) cc_final: 0.9127 (tt) REVERT: 4 8 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (p) REVERT: 4 10 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8416 (mttt) REVERT: 6 12 LYS cc_start: 0.8826 (mttt) cc_final: 0.8359 (mtpt) REVERT: 7 55 MET cc_start: 0.7283 (tmm) cc_final: 0.7067 (tmm) outliers start: 267 outliers final: 215 residues processed: 1252 average time/residue: 1.2186 time to fit residues: 2656.1874 Evaluate side-chains 1305 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1071 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 114 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 47 LYS Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 8 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 40 GLN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 69 VAL Chi-restraints excluded: chain i residue 90 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 61 SER Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 84 SER Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 87 ILE Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 45 ASN Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 78 ARG Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 38 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 9 THR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 70 ARG Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 43 THR Chi-restraints excluded: chain 7 residue 53 SER Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 853 optimal weight: 10.0000 chunk 898 optimal weight: 8.9990 chunk 819 optimal weight: 0.4980 chunk 873 optimal weight: 5.9990 chunk 526 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 686 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 789 optimal weight: 0.0980 chunk 826 optimal weight: 5.9990 chunk 870 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 52 GLN o 46 HIS ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN F 75 GLN H 64 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN ** 2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN 7 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.711 152930 Z= 0.348 Angle : 0.673 84.746 229029 Z= 0.323 Chirality : 0.033 0.725 29331 Planarity : 0.005 0.126 12042 Dihedral : 22.923 177.762 76873 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.39 % Favored : 90.50 % Rotamer: Outliers : 4.73 % Allowed : 24.96 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % 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: -2.46 (0.11), residues: 5292 helix: -0.06 (0.13), residues: 1481 sheet: -1.80 (0.17), residues: 872 loop : -2.50 (0.10), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 41 HIS 0.015 0.001 HIS 5 45 PHE 0.029 0.001 PHE 3 78 TYR 0.024 0.002 TYR E 59 ARG 0.008 0.000 ARG 7 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1144 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 114 ILE cc_start: 0.5964 (mt) cc_final: 0.5648 (mt) REVERT: b 154 MET cc_start: 0.6199 (tpp) cc_final: 0.5238 (ttt) REVERT: b 168 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7357 (tttt) REVERT: b 199 VAL cc_start: 0.7935 (t) cc_final: 0.7685 (m) REVERT: b 207 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7040 (mt) REVERT: b 216 LYS cc_start: 0.6694 (pttt) cc_final: 0.5912 (pttm) REVERT: c 34 GLU cc_start: 0.8005 (pt0) cc_final: 0.7222 (pt0) REVERT: d 8 ASN cc_start: 0.6475 (m110) cc_final: 0.6166 (m110) REVERT: e 14 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7466 (mtm-85) REVERT: e 52 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (ptpt) REVERT: f 65 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7338 (p) REVERT: g 73 LEU cc_start: 0.7920 (mm) cc_final: 0.7300 (tt) REVERT: h 16 ASN cc_start: 0.8682 (m-40) cc_final: 0.8434 (m110) REVERT: h 24 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8564 (ptpp) REVERT: h 70 ASP cc_start: 0.6724 (t0) cc_final: 0.6191 (t0) REVERT: h 94 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7377 (pmm) REVERT: i 39 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6697 (tp30) REVERT: i 101 LYS cc_start: 0.6966 (mmmt) cc_final: 0.6586 (mmmt) REVERT: j 64 GLN cc_start: 0.8177 (pp30) cc_final: 0.7810 (pp30) REVERT: j 67 GLN cc_start: 0.7871 (tt0) cc_final: 0.7635 (tt0) REVERT: j 68 ARG cc_start: 0.5948 (tmm160) cc_final: 0.5603 (ttp80) REVERT: j 73 LEU cc_start: 0.8750 (mt) cc_final: 0.8411 (mt) REVERT: k 57 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8228 (mttt) REVERT: l 35 PHE cc_start: 0.1914 (OUTLIER) cc_final: 0.0427 (m-80) REVERT: m 42 ASP cc_start: 0.3378 (t70) cc_final: 0.2939 (t0) REVERT: m 81 MET cc_start: 0.6345 (tmm) cc_final: 0.5983 (ptm) REVERT: n 34 TYR cc_start: 0.7967 (m-80) cc_final: 0.7702 (m-80) REVERT: o 11 ILE cc_start: 0.8026 (pt) cc_final: 0.7742 (mm) REVERT: p 6 ARG cc_start: 0.7944 (ptt180) cc_final: 0.7523 (ptt90) REVERT: p 15 ASN cc_start: 0.8691 (m-40) cc_final: 0.8304 (m-40) REVERT: D 32 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (mp) REVERT: D 42 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8460 (ptp-170) REVERT: D 254 LEU cc_start: 0.7856 (mt) cc_final: 0.7390 (mt) REVERT: E 122 SER cc_start: 0.9489 (t) cc_final: 0.9167 (m) REVERT: E 198 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8122 (tptt) REVERT: H 98 MET cc_start: 0.5917 (tpt) cc_final: 0.5603 (tpt) REVERT: H 99 GLN cc_start: 0.7156 (mp10) cc_final: 0.6907 (mp10) REVERT: M 38 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7514 (tmm160) REVERT: N 13 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7257 (p0) REVERT: Q 45 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7014 (mt-10) REVERT: Q 52 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8447 (mtmm) REVERT: Q 94 THR cc_start: 0.8167 (p) cc_final: 0.7944 (p) REVERT: Q 112 ASP cc_start: 0.8851 (p0) cc_final: 0.8280 (p0) REVERT: Q 120 GLU cc_start: 0.8347 (pm20) cc_final: 0.7941 (pm20) REVERT: S 4 HIS cc_start: 0.7115 (t-90) cc_final: 0.6859 (t-90) REVERT: T 74 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7219 (tmm) REVERT: U 23 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: V 40 ASN cc_start: 0.6871 (p0) cc_final: 0.6580 (p0) REVERT: X 31 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: Y 47 GLU cc_start: 0.7293 (mp0) cc_final: 0.6887 (mp0) REVERT: 1 16 GLU cc_start: 0.7653 (tp30) cc_final: 0.7366 (tp30) REVERT: 1 30 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7396 (t80) REVERT: 1 43 ILE cc_start: 0.8729 (mm) cc_final: 0.8527 (mm) REVERT: 1 50 ILE cc_start: 0.9327 (mt) cc_final: 0.8985 (tt) REVERT: 1 54 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: 4 8 THR cc_start: 0.9188 (m) cc_final: 0.8921 (p) REVERT: 4 10 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8524 (mttt) REVERT: 6 12 LYS cc_start: 0.8850 (mttt) cc_final: 0.8417 (mtpt) REVERT: 6 32 LEU cc_start: 0.9277 (mt) cc_final: 0.9026 (mm) outliers start: 216 outliers final: 166 residues processed: 1250 average time/residue: 1.2745 time to fit residues: 2771.3941 Evaluate side-chains 1267 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1086 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 40 GLN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 84 SER Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 87 ILE Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 54 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 3 residue 14 PHE Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 50 ILE Chi-restraints excluded: chain 3 residue 70 ARG Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 573 optimal weight: 10.0000 chunk 924 optimal weight: 20.0000 chunk 564 optimal weight: 20.0000 chunk 438 optimal weight: 10.0000 chunk 642 optimal weight: 10.0000 chunk 969 optimal weight: 8.9990 chunk 892 optimal weight: 0.9990 chunk 771 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 596 optimal weight: 50.0000 chunk 473 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN i 70 HIS ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 GLN ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN H 64 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.718 152930 Z= 0.446 Angle : 0.790 84.102 229029 Z= 0.379 Chirality : 0.039 0.708 29331 Planarity : 0.006 0.126 12042 Dihedral : 22.961 178.976 76873 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.81 % Favored : 88.06 % Rotamer: Outliers : 5.08 % Allowed : 25.25 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.11), residues: 5292 helix: -0.21 (0.13), residues: 1463 sheet: -1.98 (0.16), residues: 878 loop : -2.54 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP c 18 HIS 0.016 0.002 HIS U 88 PHE 0.030 0.002 PHE 3 78 TYR 0.028 0.002 TYR W 68 ARG 0.013 0.001 ARG D 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1078 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.3978 (pmm) cc_final: 0.2649 (tmm) REVERT: b 114 ILE cc_start: 0.6118 (mt) cc_final: 0.5772 (mt) REVERT: b 154 MET cc_start: 0.6265 (tpp) cc_final: 0.5165 (ttt) REVERT: b 168 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7409 (tttt) REVERT: b 199 VAL cc_start: 0.8007 (t) cc_final: 0.7793 (m) REVERT: b 207 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.6932 (mt) REVERT: c 69 THR cc_start: 0.6401 (t) cc_final: 0.5815 (m) REVERT: c 200 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.6924 (m100) REVERT: d 8 ASN cc_start: 0.6527 (m110) cc_final: 0.6259 (m110) REVERT: d 55 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: e 52 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8247 (ptpt) REVERT: f 65 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (p) REVERT: g 73 LEU cc_start: 0.7975 (mm) cc_final: 0.7260 (tt) REVERT: h 16 ASN cc_start: 0.8866 (m-40) cc_final: 0.8619 (m110) REVERT: h 70 ASP cc_start: 0.6972 (t0) cc_final: 0.6397 (t0) REVERT: h 94 MET cc_start: 0.7972 (pmm) cc_final: 0.7292 (pmm) REVERT: i 101 LYS cc_start: 0.6993 (mmmt) cc_final: 0.6610 (mmmt) REVERT: j 64 GLN cc_start: 0.8022 (pp30) cc_final: 0.7495 (pp30) REVERT: j 73 LEU cc_start: 0.8769 (mt) cc_final: 0.8456 (mt) REVERT: l 35 PHE cc_start: 0.1860 (OUTLIER) cc_final: 0.0541 (m-80) REVERT: m 42 ASP cc_start: 0.3633 (t70) cc_final: 0.3223 (t0) REVERT: n 34 TYR cc_start: 0.8009 (m-80) cc_final: 0.7768 (m-80) REVERT: p 15 ASN cc_start: 0.8855 (m-40) cc_final: 0.8469 (m-40) REVERT: r 57 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7699 (tp40) REVERT: D 32 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 42 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8569 (ptp-170) REVERT: E 122 SER cc_start: 0.9518 (t) cc_final: 0.9227 (m) REVERT: E 198 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7885 (tttt) REVERT: M 38 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7462 (tmm160) REVERT: N 13 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7521 (p0) REVERT: Q 45 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7055 (mt-10) REVERT: Q 52 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8450 (mtmm) REVERT: Q 112 ASP cc_start: 0.8829 (p0) cc_final: 0.8335 (p0) REVERT: Q 120 GLU cc_start: 0.8539 (pm20) cc_final: 0.8256 (pm20) REVERT: T 55 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7001 (ttm110) REVERT: T 74 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7374 (tmm) REVERT: U 23 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: U 78 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8253 (ptt90) REVERT: V 40 ASN cc_start: 0.7230 (p0) cc_final: 0.6876 (p0) REVERT: X 31 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: Y 47 GLU cc_start: 0.7304 (mp0) cc_final: 0.6840 (mp0) REVERT: 1 16 GLU cc_start: 0.7589 (tp30) cc_final: 0.7237 (tp30) REVERT: 1 30 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7568 (t80) REVERT: 4 8 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8979 (p) REVERT: 4 10 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8414 (mttt) REVERT: 5 19 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6363 (p) outliers start: 232 outliers final: 193 residues processed: 1192 average time/residue: 1.2289 time to fit residues: 2540.7480 Evaluate side-chains 1256 residues out of total 4571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1044 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 8 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 14 VAL Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 70 HIS Chi-restraints excluded: chain i residue 99 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 35 PHE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 113 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 84 SER Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain q residue 87 ILE Chi-restraints excluded: chain r residue 28 TYR Chi-restraints excluded: chain r residue 57 GLN Chi-restraints excluded: chain r residue 69 HIS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 26 TYR Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 106 GLN Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 37 GLN Chi-restraints excluded: chain T residue 42 SER Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 78 ARG Chi-restraints excluded: chain V residue 35 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 ASP Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 68 VAL Chi-restraints excluded: chain X residue 83 TYR Chi-restraints excluded: chain Y residue 8 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 92 VAL Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 39 ASP Chi-restraints excluded: chain 2 residue 40 ASN Chi-restraints excluded: chain 3 residue 14 PHE Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 70 ARG Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 30 CYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 44 LEU Chi-restraints excluded: chain 8 residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 613 optimal weight: 20.0000 chunk 822 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 711 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 214 optimal weight: 7.9990 chunk 773 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 70 HIS ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 GLN t 21 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN 4 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099764 restraints weight = 377646.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100229 restraints weight = 217832.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100706 restraints weight = 183375.986| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.716 152930 Z= 0.415 Angle : 0.764 84.265 229029 Z= 0.368 Chirality : 0.038 0.716 29331 Planarity : 0.005 0.127 12042 Dihedral : 22.989 178.606 76873 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.30 % Favored : 88.59 % Rotamer: Outliers : 5.23 % Allowed : 25.57 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 1.09 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.11), residues: 5292 helix: -0.24 (0.13), residues: 1463 sheet: -1.96 (0.17), residues: 863 loop : -2.57 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP c 18 HIS 0.017 0.002 HIS U 88 PHE 0.025 0.002 PHE f 26 TYR 0.033 0.002 TYR r 56 ARG 0.016 0.001 ARG 0 37 Origin is already at (0, 0, 0), no shifts will be applied External origin is not on a grid point...ignoring external origin ***Please contact the Phenix developers if you need Phenix to use this external_origin*** =============================================================================== Job complete usr+sys time: 37765.06 seconds wall clock time: 657 minutes 46.64 seconds (39466.64 seconds total)