Starting phenix.real_space_refine on Thu Feb 29 20:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msh_23962/02_2024/7msh_23962_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 4839 5.49 5 Mg 420 5.21 5 S 101 5.16 5 C 76118 2.51 5 N 28401 2.21 5 O 42218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "O PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "x ARG 12": "NH1" <-> "NH2" Residue "x ARG 233": "NH1" <-> "NH2" Residue "x ARG 257": "NH1" <-> "NH2" Residue "x ARG 265": "NH1" <-> "NH2" Residue "x ARG 302": "NH1" <-> "NH2" Residue "x ARG 334": "NH1" <-> "NH2" Residue "x ARG 346": "NH1" <-> "NH2" Residue "x ARG 539": "NH1" <-> "NH2" Residue "x ARG 553": "NH1" <-> "NH2" Residue "x ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152103 Number of models: 1 Model: "" Number of chains: 71 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "7" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66958 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 1, 'rna2p_pur': 294, 'rna2p_pyr': 158, 'rna3p': 1, 'rna3p_pur': 1488, 'rna3p_pyr': 1176} Link IDs: {'rna2p': 453, 'rna3p': 2664} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 45} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 537 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 93, 'rna3p': 6, 'rna3p_pur': 732, 'rna3p_pyr': 569} Link IDs: {'rna2p': 212, 'rna3p': 1306} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "x" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4297 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 1 Chain: "y" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1602 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 63} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 286 Unusual residues: {' MG': 286} Classifications: {'undetermined': 286} Link IDs: {None: 285} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Unusual residues: {' MG': 121} Classifications: {'undetermined': 121} Link IDs: {None: 120} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 119.706 179.834 187.383 1.00 65.38 S ATOM 519 SG CYS 1 18 119.857 183.331 185.473 1.00 64.63 S ATOM 734 SG CYS 1 42 123.252 182.327 186.155 1.00 60.44 S ATOM 755 SG CYS 1 45 121.615 183.958 188.935 1.00 62.63 S ATOM 1778 SG CYS 4 11 186.156 98.474 133.577 1.00112.19 S ATOM 1801 SG CYS 4 14 186.311 101.835 132.504 1.00111.04 S ATOM 2131 SG CYS 6 18 121.163 109.103 227.702 1.00138.05 S ATOM 2280 SG CYS 6 38 122.605 112.559 224.208 1.00131.89 S ATOM 2301 SG CYS 6 41 120.712 109.601 223.347 1.00134.60 S ATOM 94739 SG CYS X 5 94.096 202.035 122.522 1.00 53.20 S ATOM 94761 SG CYS X 8 95.634 204.154 125.178 1.00 55.64 S ATOM 95104 SG CYS X 52 93.765 200.635 126.480 1.00 56.38 S ATOM 95123 SG CYS X 55 92.113 203.811 126.019 1.00 59.37 S ATOM A0VPH SG CYS n 24 89.466 56.772 170.098 1.00 78.81 S ATOM A0VQ2 SG CYS n 27 91.036 58.406 167.234 1.00 76.94 S ATOM A0VT0 SG CYS n 40 88.302 60.761 168.171 1.00 72.41 S ATOM A0VTP SG CYS n 43 87.583 57.621 166.408 1.00 73.02 S ATOM A0XRW SG CYS r 20 34.690 118.186 106.043 1.00110.91 S ATOM A0XSK SG CYS r 23 34.315 117.986 101.851 1.00116.70 S ATOM A0Y05 SG CYS r 57 38.449 118.777 103.272 1.00 95.20 S Time building chain proxies: 52.94, per 1000 atoms: 0.35 Number of scatterers: 152103 At special positions: 0 Unit cell: (242.74, 271.36, 242.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 101 16.00 P 4839 15.00 Mg 420 11.99 O 42218 8.00 N 28401 7.00 C 76118 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: 59.04 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 18 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " Number of angles added : 21 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11204 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: 177 helices and 74 sheets defined 36.3% alpha, 16.9% beta 828 base pairs and 2511 stacking pairs defined. Time for finding SS restraints: 70.23 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 4.050A pdb=" N THR 0 13 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.665A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG 0 48 " --> pdb=" O LEU 0 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY 0 50 " --> pdb=" O ALA 0 46 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 19 removed outlier: 3.748A pdb=" N ALA 2 16 " --> pdb=" O ASN 2 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL 2 18 " --> pdb=" O ARG 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 27 removed outlier: 4.142A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 41 removed outlier: 3.566A pdb=" N SER 2 32 " --> pdb=" O ARG 2 28 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 2 40 " --> pdb=" O SER 2 36 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.618A pdb=" N SER 3 11 " --> pdb=" O HIS 3 7 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 46 removed outlier: 3.703A pdb=" N ARG 3 42 " --> pdb=" O SER 3 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLY 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 3.604A pdb=" N THR 3 55 " --> pdb=" O ALA 3 51 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL 3 58 " --> pdb=" O ASP 3 54 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 3 59 " --> pdb=" O THR 3 55 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 4.576A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '7' and resid 2 through 9 removed outlier: 3.580A pdb=" N LYS 7 7 " --> pdb=" O LYS 7 3 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS 7 8 " --> pdb=" O ARG 7 4 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 7 9 " --> pdb=" O GLY 7 5 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 16 removed outlier: 4.134A pdb=" N ALA 8 11 " --> pdb=" O ALA 8 7 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA 8 12 " --> pdb=" O TYR 8 8 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA 8 13 " --> pdb=" O ARG 8 9 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS 8 14 " --> pdb=" O ALA 8 10 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 38 removed outlier: 3.610A pdb=" N ALA 8 27 " --> pdb=" O PRO 8 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA 8 30 " --> pdb=" O ALA 8 26 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS 8 37 " --> pdb=" O THR 8 33 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN 8 38 " --> pdb=" O SER 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 3.947A pdb=" N ASP 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 8 86 " --> pdb=" O GLU 8 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA 8 87 " --> pdb=" O LYS 8 83 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA 8 89 " --> pdb=" O ASP 8 85 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 86 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY 8 91 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) Processing helix chain '8' and resid 99 through 107 removed outlier: 3.986A pdb=" N ARG 8 103 " --> pdb=" O ASP 8 99 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN 8 105 " --> pdb=" O ILE 8 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY 8 106 " --> pdb=" O GLU 8 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 129 removed outlier: 4.872A pdb=" N ARG 8 126 " --> pdb=" O ALA 8 122 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE 8 127 " --> pdb=" O LYS 8 123 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 135 removed outlier: 3.751A pdb=" N ARG 8 134 " --> pdb=" O VAL 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 148 through 159 removed outlier: 4.138A pdb=" N ALA 8 152 " --> pdb=" O ASP 8 148 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP 8 155 " --> pdb=" O LYS 8 151 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE 8 156 " --> pdb=" O ALA 8 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS 8 157 " --> pdb=" O VAL 8 153 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 4.207A pdb=" N LEU 8 185 " --> pdb=" O ASP 8 181 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA 8 186 " --> pdb=" O GLU 8 182 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU 8 187 " --> pdb=" O LYS 8 183 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN 8 188 " --> pdb=" O LEU 8 184 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA 8 191 " --> pdb=" O GLU 8 187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA 8 192 " --> pdb=" O ASN 8 188 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE 8 193 " --> pdb=" O TYR 8 189 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP 8 194 " --> pdb=" O GLY 8 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.798A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.448A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.510A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 5.432A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.533A pdb=" N GLN C 201 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.550A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 4.090A pdb=" N HIS D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.529A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.509A pdb=" N MET E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLN E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.464A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.645A pdb=" N ALA E 116 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 4.125A pdb=" N ALA E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 149 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.640A pdb=" N LYS E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 4.999A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.811A pdb=" N ASN E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.361A pdb=" N GLU F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 68 removed outlier: 4.013A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.652A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.792A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.913A pdb=" N ALA F 50 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG F 52 " --> pdb=" O GLU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.716A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL G 77 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.670A pdb=" N GLN G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.964A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 removed outlier: 4.242A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.530A pdb=" N ALA J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 71 removed outlier: 3.904A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.551A pdb=" N LEU J 92 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.096A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.233A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.658A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 110' Processing helix chain 'K' and resid 111 through 118 removed outlier: 3.533A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 removed outlier: 3.639A pdb=" N LEU L 8 " --> pdb=" O LYS L 4 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG L 9 " --> pdb=" O LEU L 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 4 through 9' Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.006A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 4.001A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.587A pdb=" N ASN L 83 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.759A pdb=" N LEU L 97 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 98 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.752A pdb=" N ARG L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY L 140 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.707A pdb=" N ALA M 50 " --> pdb=" O GLN M 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 4.625A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 31 removed outlier: 3.631A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.643A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.623A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE N 52 " --> pdb=" O ALA N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 3.919A pdb=" N LYS N 68 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.556A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 4.030A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 3.699A pdb=" N ARG O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 3.859A pdb=" N ARG O 66 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 62 through 68' Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.613A pdb=" N ARG O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU O 85 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG O 86 " --> pdb=" O LEU O 82 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.797A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 9 removed outlier: 4.058A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 103 removed outlier: 5.391A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 4.457A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG Q 15 " --> pdb=" O HIS Q 11 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.116A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.652A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP Q 49 " --> pdb=" O TYR Q 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 59 " --> pdb=" O GLY Q 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Q 60 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.793A pdb=" N ILE Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.671A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 removed outlier: 3.546A pdb=" N THR Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA Q 113 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 removed outlier: 4.304A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 3.602A pdb=" N ARG S 29 " --> pdb=" O ARG S 25 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 4.193A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP S 48 " --> pdb=" O ASP S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 71 removed outlier: 3.858A pdb=" N VAL S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA S 58 " --> pdb=" O SER S 54 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA S 66 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN S 71 " --> pdb=" O ASN S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.746A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.157A pdb=" N TYR T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 removed outlier: 3.668A pdb=" N ILE T 42 " --> pdb=" O ASN T 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.318A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 removed outlier: 3.766A pdb=" N SER V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG V 24 " --> pdb=" O GLY V 20 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA V 28 " --> pdb=" O ARG V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 59 removed outlier: 5.674A pdb=" N TYR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 3.788A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 3.750A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 13' Processing helix chain 'Y' and resid 14 through 39 removed outlier: 6.086A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU Y 24 " --> pdb=" O GLU Y 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN Y 35 " --> pdb=" O ASN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.809A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL Y 60 " --> pdb=" O ARG Y 56 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Y 66 " --> pdb=" O ARG Y 62 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 4.537A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR Z 25 " --> pdb=" O GLU Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.673A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.042A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.552A pdb=" N TYR c 31 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL c 32 " --> pdb=" O TYR c 28 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 3.721A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 72 through 77' Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.916A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG c 87 " --> pdb=" O ALA c 83 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU c 93 " --> pdb=" O ASP c 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.032A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.664A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 4.121A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.961A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.520A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 4.573A pdb=" N LEU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN d 49 " --> pdb=" O GLU d 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS d 55 " --> pdb=" O GLN d 51 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.978A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.459A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE d 88 " --> pdb=" O GLU d 84 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.679A pdb=" N ARG d 99 " --> pdb=" O ASN d 95 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.781A pdb=" N GLN d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU d 112 " --> pdb=" O MET d 108 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 removed outlier: 3.857A pdb=" N ILE d 152 " --> pdb=" O VAL d 148 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 148 through 157' Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.614A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 4.250A pdb=" N ALA e 92 " --> pdb=" O PRO e 88 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS e 93 " --> pdb=" O ALA e 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.309A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS e 148 " --> pdb=" O ALA e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 4.820A pdb=" N VAL e 167 " --> pdb=" O ASN e 163 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL e 168 " --> pdb=" O ALA e 164 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 4.749A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 197 removed outlier: 4.128A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA e 196 " --> pdb=" O ILE e 192 " (cutoff:3.500A) Proline residue: e 197 - end of helix No H-bonds generated for 'chain 'e' and resid 191 through 197' Processing helix chain 'e' and resid 198 through 209 removed outlier: 3.748A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA e 203 " --> pdb=" O GLY e 199 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU e 208 " --> pdb=" O ARG e 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 34 removed outlier: 4.104A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG f 31 " --> pdb=" O LEU f 27 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY f 34 " --> pdb=" O VAL f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 82 removed outlier: 3.723A pdb=" N SER f 73 " --> pdb=" O PRO f 69 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU f 74 " --> pdb=" O ALA f 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.917A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.949A pdb=" N ARG g 41 " --> pdb=" O SER g 37 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE g 42 " --> pdb=" O LEU g 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL g 43 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.742A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.199A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.533A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.889A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.629A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.896A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 4.155A pdb=" N ARG h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN h 121 " --> pdb=" O GLN h 117 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY h 122 " --> pdb=" O ALA h 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 61 Proline residue: i 61 - end of helix Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.980A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN i 67 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 4.024A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL i 76 " --> pdb=" O PRO i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.552A pdb=" N LEU i 100 " --> pdb=" O GLN i 96 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU i 108 " --> pdb=" O ILE i 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.906A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 34 removed outlier: 3.964A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA j 34 " --> pdb=" O VAL j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.715A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 3.767A pdb=" N VAL k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 61' Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.559A pdb=" N ARG k 82 " --> pdb=" O GLU k 78 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 4.646A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER k 109 " --> pdb=" O THR k 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU k 110 " --> pdb=" O ALA k 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN k 111 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA k 112 " --> pdb=" O ARG k 108 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 4.190A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.520A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 21 removed outlier: 3.714A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.135A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA m 35 " --> pdb=" O ASN m 31 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.872A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN m 63 " --> pdb=" O TYR m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.722A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP m 77 " --> pdb=" O GLU m 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE m 78 " --> pdb=" O VAL m 74 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE m 82 " --> pdb=" O ILE m 78 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.778A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.600A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.578A pdb=" N VAL n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS n 9 " --> pdb=" O ALA n 5 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.843A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.694A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.528A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS o 44 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.056A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.967A pdb=" N SER o 80 " --> pdb=" O GLU o 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.835A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER p 61 " --> pdb=" O GLN p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 4.029A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU p 73 " --> pdb=" O PRO p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 3.575A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.708A pdb=" N VAL p 105 " --> pdb=" O SER p 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA p 111 " --> pdb=" O ASN p 107 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA p 112 " --> pdb=" O ALA p 108 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP p 114 " --> pdb=" O LEU p 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 3.546A pdb=" N ALA r 24 " --> pdb=" O CYS r 20 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 40 removed outlier: 4.982A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.960A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.582A pdb=" N GLN r 61 " --> pdb=" O CYS r 57 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 4.380A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.711A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 7 through 42 removed outlier: 3.797A pdb=" N ARG t 12 " --> pdb=" O GLN t 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR t 13 " --> pdb=" O LYS t 9 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU t 19 " --> pdb=" O GLU t 15 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG t 20 " --> pdb=" O ARG t 16 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS t 25 " --> pdb=" O ASN t 21 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR t 30 " --> pdb=" O SER t 26 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA t 31 " --> pdb=" O SER t 27 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS t 40 " --> pdb=" O ARG t 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA t 41 " --> pdb=" O GLU t 37 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.122A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS t 57 " --> pdb=" O SER t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.571A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA t 73 " --> pdb=" O LYS t 69 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA t 78 " --> pdb=" O ASN t 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'x' and resid 43 through 53 removed outlier: 3.597A pdb=" N LEU x 48 " --> pdb=" O LYS x 44 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE x 50 " --> pdb=" O SER x 46 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA x 52 " --> pdb=" O LEU x 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY x 53 " --> pdb=" O ARG x 49 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 92 removed outlier: 4.196A pdb=" N GLY x 87 " --> pdb=" O LYS x 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN x 88 " --> pdb=" O THR x 84 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL x 89 " --> pdb=" O VAL x 85 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU x 90 " --> pdb=" O ARG x 86 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU x 91 " --> pdb=" O GLY x 87 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY x 92 " --> pdb=" O ASN x 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 83 through 92' Processing helix chain 'x' and resid 93 through 108 removed outlier: 4.223A pdb=" N LYS x 97 " --> pdb=" O MET x 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE x 98 " --> pdb=" O GLY x 94 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS x 99 " --> pdb=" O ASP x 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP x 101 " --> pdb=" O LYS x 97 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG x 102 " --> pdb=" O ILE x 98 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE x 103 " --> pdb=" O LYS x 99 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA x 107 " --> pdb=" O PHE x 103 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU x 108 " --> pdb=" O ASN x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 116 through 133 removed outlier: 5.211A pdb=" N GLU x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU x 121 " --> pdb=" O GLU x 117 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET x 122 " --> pdb=" O LEU x 118 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY x 123 " --> pdb=" O MET x 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG x 124 " --> pdb=" O GLU x 120 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP x 130 " --> pdb=" O GLN x 126 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS x 131 " --> pdb=" O GLU x 127 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA x 132 " --> pdb=" O GLU x 128 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP x 133 " --> pdb=" O LEU x 129 " (cutoff:3.500A) Processing helix chain 'x' and resid 136 through 149 removed outlier: 6.474A pdb=" N GLN x 140 " --> pdb=" O ASP x 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU x 141 " --> pdb=" O LEU x 137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU x 142 " --> pdb=" O ASP x 138 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN x 143 " --> pdb=" O ALA x 139 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA x 144 " --> pdb=" O GLN x 140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET x 145 " --> pdb=" O LEU x 141 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA x 147 " --> pdb=" O GLN x 143 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU x 148 " --> pdb=" O ALA x 144 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG x 149 " --> pdb=" O MET x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 163 through 177 removed outlier: 4.557A pdb=" N ARG x 167 " --> pdb=" O GLY x 163 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS x 171 " --> pdb=" O ARG x 167 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU x 173 " --> pdb=" O ALA x 169 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU x 174 " --> pdb=" O LEU x 170 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU x 175 " --> pdb=" O CYS x 171 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER x 176 " --> pdb=" O LYS x 172 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS x 177 " --> pdb=" O LEU x 173 " (cutoff:3.500A) Processing helix chain 'x' and resid 191 through 205 removed outlier: 3.708A pdb=" N VAL x 195 " --> pdb=" O ASP x 191 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN x 196 " --> pdb=" O ALA x 192 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN x 200 " --> pdb=" O GLN x 196 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER x 204 " --> pdb=" O GLN x 200 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR x 205 " --> pdb=" O HIS x 201 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 221 removed outlier: 3.964A pdb=" N LEU x 219 " --> pdb=" O ASP x 215 " (cutoff:3.500A) Processing helix chain 'x' and resid 242 through 271 removed outlier: 3.657A pdb=" N GLU x 246 " --> pdb=" O SER x 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL x 254 " --> pdb=" O GLU x 250 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG x 257 " --> pdb=" O ALA x 253 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS x 258 " --> pdb=" O VAL x 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP x 259 " --> pdb=" O GLN x 255 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA x 260 " --> pdb=" O GLY x 256 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS x 261 " --> pdb=" O ARG x 257 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR x 267 " --> pdb=" O GLN x 263 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA x 271 " --> pdb=" O THR x 267 " (cutoff:3.500A) Processing helix chain 'x' and resid 283 through 303 removed outlier: 3.523A pdb=" N ARG x 287 " --> pdb=" O LYS x 283 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN x 289 " --> pdb=" O LYS x 285 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG x 290 " --> pdb=" O ALA x 286 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR x 291 " --> pdb=" O ARG x 287 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET x 294 " --> pdb=" O ARG x 290 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU x 297 " --> pdb=" O GLU x 293 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU x 299 " --> pdb=" O ALA x 295 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS x 300 " --> pdb=" O ALA x 296 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR x 301 " --> pdb=" O GLU x 297 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG x 302 " --> pdb=" O ALA x 298 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS x 303 " --> pdb=" O GLU x 299 " (cutoff:3.500A) Processing helix chain 'x' and resid 359 through 369 removed outlier: 3.537A pdb=" N LEU x 363 " --> pdb=" O GLY x 359 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE x 364 " --> pdb=" O LYS x 360 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS x 365 " --> pdb=" O THR x 361 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE x 367 " --> pdb=" O LEU x 363 " (cutoff:3.500A) Processing helix chain 'x' and resid 401 through 407 removed outlier: 3.681A pdb=" N VAL x 406 " --> pdb=" O VAL x 402 " (cutoff:3.500A) Processing helix chain 'x' and resid 421 through 430 removed outlier: 3.572A pdb=" N VAL x 426 " --> pdb=" O SER x 422 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER x 427 " --> pdb=" O ARG x 423 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE x 429 " --> pdb=" O TYR x 425 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY x 430 " --> pdb=" O VAL x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 439 through 444 removed outlier: 4.009A pdb=" N LEU x 443 " --> pdb=" O PRO x 439 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER x 444 " --> pdb=" O ALA x 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 439 through 444' Processing helix chain 'x' and resid 445 through 458 removed outlier: 3.538A pdb=" N ASN x 449 " --> pdb=" O GLY x 445 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU x 451 " --> pdb=" O GLU x 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN x 452 " --> pdb=" O ARG x 448 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU x 453 " --> pdb=" O ASN x 449 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA x 454 " --> pdb=" O ARG x 450 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR x 456 " --> pdb=" O ASN x 452 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS x 458 " --> pdb=" O ALA x 454 " (cutoff:3.500A) Processing helix chain 'x' and resid 474 through 489 removed outlier: 3.501A pdb=" N SER x 480 " --> pdb=" O GLU x 476 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA x 484 " --> pdb=" O SER x 480 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU x 486 " --> pdb=" O GLU x 482 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN x 487 " --> pdb=" O ASN x 483 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE x 488 " --> pdb=" O ALA x 484 " (cutoff:3.500A) Proline residue: x 489 - end of helix Processing helix chain 'x' and resid 498 through 506 removed outlier: 3.671A pdb=" N ASP x 503 " --> pdb=" O ARG x 499 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG x 504 " --> pdb=" O TRP x 500 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS x 506 " --> pdb=" O LEU x 502 " (cutoff:3.500A) Processing helix chain 'x' and resid 528 through 540 removed outlier: 3.566A pdb=" N GLU x 533 " --> pdb=" O PHE x 529 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU x 534 " --> pdb=" O GLY x 530 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL x 537 " --> pdb=" O GLU x 533 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) Processing helix chain 'x' and resid 433 through 438 removed outlier: 3.649A pdb=" N GLN x 437 " --> pdb=" O PRO x 434 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS x 438 " --> pdb=" O ASP x 435 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 Processing sheet with id= 2, first strand: chain '1' and resid 8 through 13 removed outlier: 3.823A pdb=" N LYS 1 27 " --> pdb=" O PRO 1 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 37 through 40 Processing sheet with id= 4, first strand: chain '3' and resid 22 through 25 removed outlier: 6.242A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 42 through 47 removed outlier: 4.277A pdb=" N LYS 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 93 through 97 removed outlier: 3.614A pdb=" N VAL 8 94 " --> pdb=" O VAL 8 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL 8 77 " --> pdb=" O VAL 8 94 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA 8 79 " --> pdb=" O GLY 8 96 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.611A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.620A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.892A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.197A pdb=" N ASN C 129 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 138 through 141 removed outlier: 7.588A pdb=" N ALA C 138 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY C 167 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS C 168 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.674A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL D 175 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.994A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 16 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D 18 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 194 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.127A pdb=" N GLN D 99 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 38 through 42 removed outlier: 5.092A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR D 47 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.401A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.963A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 13 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.605A pdb=" N VAL E 200 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 184 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 72 through 76 removed outlier: 3.751A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN F 44 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP F 160 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU F 139 " --> pdb=" O MET F 159 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 79 through 82 removed outlier: 7.610A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 41 through 46 removed outlier: 4.162A pdb=" N LYS G 42 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G 46 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 104 through 107 removed outlier: 4.371A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE G 116 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 130 through 137 removed outlier: 5.723A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET G 88 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL G 134 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR G 86 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY G 136 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 164 " --> pdb=" O GLU G 89 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.677A pdb=" N LEU H 35 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.917A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.595A pdb=" N ILE K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 29, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.226A pdb=" N ARG K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE K 77 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 31, first strand: chain 'M' and resid 38 through 42 removed outlier: 7.040A pdb=" N GLU M 38 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL M 97 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU M 74 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 62 through 66 removed outlier: 3.892A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 32 through 37 removed outlier: 8.055A pdb=" N GLY N 32 " --> pdb=" O LEU N 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU N 115 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.580A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU O 46 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.667A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.952A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.793A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 20 through 25 removed outlier: 4.241A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL R 36 " --> pdb=" O GLY R 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 70 through 80 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'S' and resid 11 through 18 removed outlier: 3.557A pdb=" N ALA S 13 " --> pdb=" O VAL S 117 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 83 through 89 removed outlier: 3.690A pdb=" N THR S 83 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.297A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 25 through 28 removed outlier: 4.001A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG U 32 " --> pdb=" O TYR U 27 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.588A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU V 9 " --> pdb=" O THR V 66 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 42 through 45 removed outlier: 3.675A pdb=" N ALA V 93 " --> pdb=" O PRO V 32 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA V 80 " --> pdb=" O ASP V 94 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 120 through 125 removed outlier: 7.631A pdb=" N VAL V 176 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 127 through 132 removed outlier: 5.430A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE V 131 " --> pdb=" O VAL V 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL V 144 " --> pdb=" O VAL V 111 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU V 113 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE V 146 " --> pdb=" O GLU V 113 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN V 115 " --> pdb=" O ILE V 146 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 49, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.075A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.373A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.086A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 165 through 169 removed outlier: 3.816A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE c 196 " --> pdb=" O ALA c 189 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP c 206 " --> pdb=" O ARG c 179 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG c 179 " --> pdb=" O ASP c 206 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 136 through 139 removed outlier: 4.264A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.727A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 115 through 119 removed outlier: 3.686A pdb=" N VAL e 125 " --> pdb=" O GLY e 118 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE e 154 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 63 through 72 removed outlier: 4.003A pdb=" N ALA e 66 " --> pdb=" O GLY e 82 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL e 68 " --> pdb=" O GLY e 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY e 80 " --> pdb=" O VAL e 68 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.524A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE f 9 " --> pdb=" O ARG f 87 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 40 through 44 removed outlier: 3.965A pdb=" N ASP f 41 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL f 62 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.044A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.705A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.679A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.794A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'k' and resid 29 through 36 removed outlier: 3.607A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 90 through 93 removed outlier: 4.011A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.776A pdb=" N GLY l 32 " --> pdb=" O VAL l 80 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.842A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR l 38 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA l 53 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.694A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY p 38 " --> pdb=" O VAL p 20 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 58 through 63 removed outlier: 5.398A pdb=" N LYS q 58 " --> pdb=" O GLU q 115 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL q 128 " --> pdb=" O SER q 112 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 48 through 52 Processing sheet with id= 71, first strand: chain 'x' and resid 25 through 29 removed outlier: 4.213A pdb=" N LEU x 26 " --> pdb=" O MET x 8 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR x 6 " --> pdb=" O PHE x 28 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP x 61 " --> pdb=" O LYS x 9 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 69 through 73 removed outlier: 3.703A pdb=" N VAL x 212 " --> pdb=" O LEU x 183 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA x 32 " --> pdb=" O GLY x 207 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU x 224 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP x 230 " --> pdb=" O ARG x 233 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 321 through 325 removed outlier: 6.805A pdb=" N VAL x 321 " --> pdb=" O GLY x 381 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY x 381 " --> pdb=" O VAL x 321 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER x 377 " --> pdb=" O ASP x 325 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 385 through 390 removed outlier: 3.653A pdb=" N VAL x 389 " --> pdb=" O LEU x 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP x 467 " --> pdb=" O VAL x 389 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS x 491 " --> pdb=" O ASN x 462 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY x 348 " --> pdb=" O GLY x 490 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA x 492 " --> pdb=" O GLY x 348 " (cutoff:3.500A) 1255 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1950 hydrogen bonds 3024 hydrogen bond angles 0 basepair planarities 828 basepair parallelities 2511 stacking parallelities Total time for adding SS restraints: 234.68 Time building geometry restraints manager: 64.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12820 1.30 - 1.42: 73815 1.42 - 1.55: 68333 1.55 - 1.68: 9676 1.68 - 1.81: 170 Bond restraints: 164814 Sorted by residual: bond pdb=" C2' ANP x 601 " pdb=" C3' ANP x 601 " ideal model delta sigma weight residual 1.237 1.529 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C2' ANP x 602 " pdb=" C3' ANP x 602 " ideal model delta sigma weight residual 1.237 1.527 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.587 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 1.348 1.504 -0.156 2.00e-02 2.50e+03 6.06e+01 ... (remaining 164809 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.72: 26184 105.72 - 113.93: 104547 113.93 - 122.14: 80201 122.14 - 130.34: 33907 130.34 - 138.55: 1892 Bond angle restraints: 246731 Sorted by residual: angle pdb=" C1' G7M a 518 " pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 94.96 128.52 -33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 132.67 -24.38 3.00e+00 1.11e-01 6.60e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 119.00 23.82 3.00e+00 1.11e-01 6.30e+01 angle pdb=" C1' 2MG a 959 " pdb=" N9 2MG a 959 " pdb=" C8 2MG a 959 " ideal model delta sigma weight residual 110.07 128.50 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C1' G7M a 518 " pdb=" N9 G7M a 518 " pdb=" C4 G7M a 518 " ideal model delta sigma weight residual 142.80 125.49 17.31 3.00e+00 1.11e-01 3.33e+01 ... (remaining 246726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 94231 35.78 - 71.55: 10434 71.55 - 107.33: 1349 107.33 - 143.10: 11 143.10 - 178.88: 21 Dihedral angle restraints: 106046 sinusoidal: 88602 harmonic: 17444 Sorted by residual: dihedral pdb=" CA ALA l 113 " pdb=" C ALA l 113 " pdb=" N ARG l 114 " pdb=" CA ARG l 114 " ideal model delta harmonic sigma weight residual 180.00 130.38 49.62 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual 200.00 22.45 177.55 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a1254 " pdb=" C1' U a1254 " pdb=" N1 U a1254 " pdb=" C2 U a1254 " ideal model delta sinusoidal sigma weight residual -160.00 16.31 -176.31 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 106043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 28872 0.083 - 0.167: 2466 0.167 - 0.250: 115 0.250 - 0.333: 11 0.333 - 0.417: 6 Chirality restraints: 31470 Sorted by residual: chirality pdb=" CB ILE K 77 " pdb=" CA ILE K 77 " pdb=" CG1 ILE K 77 " pdb=" CG2 ILE K 77 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3' C a 505 " pdb=" C4' C a 505 " pdb=" O3' C a 505 " pdb=" C2' C a 505 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE c 102 " pdb=" CA ILE c 102 " pdb=" CG1 ILE c 102 " pdb=" CG2 ILE c 102 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 31467 not shown) Planarity restraints: 13363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP x 602 " 0.458 2.00e-02 2.50e+03 5.85e-01 7.70e+03 pdb=" C2' ANP x 602 " -0.610 2.00e-02 2.50e+03 pdb=" C3' ANP x 602 " -0.266 2.00e-02 2.50e+03 pdb=" C4' ANP x 602 " 0.199 2.00e-02 2.50e+03 pdb=" C5' ANP x 602 " -0.895 2.00e-02 2.50e+03 pdb=" N9 ANP x 602 " -0.015 2.00e-02 2.50e+03 pdb=" O2' ANP x 602 " -0.503 2.00e-02 2.50e+03 pdb=" O3' ANP x 602 " 0.777 2.00e-02 2.50e+03 pdb=" O4' ANP x 602 " 0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.023 2.00e-02 2.50e+03 5.38e-01 6.52e+03 pdb=" C4' OMG A2791 " 0.413 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.578 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.510 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.228 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.866 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.244 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.793 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP x 601 " -0.223 2.00e-02 2.50e+03 5.26e-01 6.22e+03 pdb=" C2' ANP x 601 " 0.277 2.00e-02 2.50e+03 pdb=" C3' ANP x 601 " 0.603 2.00e-02 2.50e+03 pdb=" C4' ANP x 601 " -0.416 2.00e-02 2.50e+03 pdb=" C5' ANP x 601 " 0.035 2.00e-02 2.50e+03 pdb=" N9 ANP x 601 " 0.770 2.00e-02 2.50e+03 pdb=" O2' ANP x 601 " -0.765 2.00e-02 2.50e+03 pdb=" O3' ANP x 601 " 0.411 2.00e-02 2.50e+03 pdb=" O4' ANP x 601 " -0.692 2.00e-02 2.50e+03 ... (remaining 13360 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1691 2.57 - 3.16: 105706 3.16 - 3.74: 278499 3.74 - 4.32: 391462 4.32 - 4.90: 545087 Nonbonded interactions: 1322445 Sorted by model distance: nonbonded pdb=" OP1 C A 807 " pdb="MG MG A3203 " model vdw 1.993 2.170 nonbonded pdb=" OP2 U A2920 " pdb="MG MG A3339 " model vdw 1.997 2.170 nonbonded pdb=" OP2 A A2208 " pdb="MG MG A3313 " model vdw 2.003 2.170 nonbonded pdb=" OP1 A A2959 " pdb="MG MG A3339 " model vdw 2.006 2.170 nonbonded pdb=" OP1 A A2014 " pdb="MG MG A3223 " model vdw 2.009 2.170 ... (remaining 1322440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.120 Extract box with map and model: 12.670 Check model and map are aligned: 1.670 Set scattering table: 1.120 Process input model: 540.750 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 565.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.008 0.292 164814 Z= 0.506 Angle : 0.894 33.561 246731 Z= 0.439 Chirality : 0.047 0.417 31470 Planarity : 0.013 0.585 13363 Dihedral : 22.509 178.879 94842 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.83 % Favored : 91.08 % Rotamer: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.08), residues: 6045 helix: -4.67 (0.05), residues: 1606 sheet: -2.38 (0.14), residues: 1067 loop : -2.91 (0.08), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP Q 61 HIS 0.019 0.003 HIS M 13 PHE 0.035 0.004 PHE e 102 TYR 0.034 0.003 TYR H 25 ARG 0.017 0.001 ARG S 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1310 time to evaluate : 6.166 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: 1 24 ILE cc_start: 0.8457 (tt) cc_final: 0.8210 (tt) REVERT: 4 22 ARG cc_start: 0.7577 (ptp-110) cc_final: 0.6804 (ptp-170) REVERT: 4 24 MET cc_start: 0.7621 (ptm) cc_final: 0.7389 (ptt) REVERT: 8 58 MET cc_start: 0.6962 (tpt) cc_final: 0.6290 (tmm) REVERT: 8 171 LEU cc_start: 0.7581 (mt) cc_final: 0.7344 (mt) REVERT: 8 181 ASP cc_start: 0.7413 (m-30) cc_final: 0.6576 (p0) REVERT: 8 183 LYS cc_start: 0.8408 (mptt) cc_final: 0.8136 (mptt) REVERT: 8 210 LYS cc_start: 0.7343 (mtmt) cc_final: 0.6939 (mtmt) REVERT: C 179 SER cc_start: 0.8266 (p) cc_final: 0.8058 (p) REVERT: E 40 MET cc_start: 0.7879 (mtm) cc_final: 0.7570 (mtp) REVERT: E 127 ASN cc_start: 0.8684 (m-40) cc_final: 0.8445 (m110) REVERT: E 178 LEU cc_start: 0.8408 (mt) cc_final: 0.8176 (mt) REVERT: F 103 MET cc_start: 0.8127 (ttp) cc_final: 0.7896 (ttp) REVERT: F 177 LEU cc_start: 0.8743 (mt) cc_final: 0.8240 (pp) REVERT: G 87 LYS cc_start: 0.7330 (tttt) cc_final: 0.7078 (mmtt) REVERT: G 90 ILE cc_start: 0.8007 (mm) cc_final: 0.7542 (mt) REVERT: G 153 ARG cc_start: 0.7509 (mmm160) cc_final: 0.6646 (tpp80) REVERT: J 108 MET cc_start: 0.8350 (mtt) cc_final: 0.8143 (mtt) REVERT: K 7 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7946 (mtt180) REVERT: K 90 ASP cc_start: 0.7713 (p0) cc_final: 0.7431 (p0) REVERT: K 97 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7200 (ttp80) REVERT: K 104 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: L 37 LYS cc_start: 0.7290 (tttt) cc_final: 0.6953 (mtmt) REVERT: L 100 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8425 (mmmt) REVERT: M 120 ARG cc_start: 0.6606 (mtt-85) cc_final: 0.6283 (mtp-110) REVERT: N 110 MET cc_start: 0.7724 (mmm) cc_final: 0.7480 (mmt) REVERT: O 30 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7354 (ttm-80) REVERT: O 44 VAL cc_start: 0.7744 (p) cc_final: 0.7506 (m) REVERT: O 60 SER cc_start: 0.8963 (m) cc_final: 0.8700 (t) REVERT: Q 21 SER cc_start: 0.8919 (m) cc_final: 0.8677 (t) REVERT: S 54 SER cc_start: 0.8432 (p) cc_final: 0.8213 (t) REVERT: S 80 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (m) REVERT: S 83 THR cc_start: 0.8546 (m) cc_final: 0.8308 (p) REVERT: U 11 VAL cc_start: 0.8553 (t) cc_final: 0.8326 (m) REVERT: U 24 LEU cc_start: 0.8385 (mt) cc_final: 0.8166 (mp) REVERT: U 72 MET cc_start: 0.8324 (mtp) cc_final: 0.8108 (mtm) REVERT: V 47 LEU cc_start: 0.6773 (mt) cc_final: 0.6223 (tt) REVERT: Y 10 LEU cc_start: 0.8811 (mt) cc_final: 0.8588 (mp) REVERT: Z 12 THR cc_start: 0.8486 (p) cc_final: 0.8256 (t) REVERT: c 97 GLN cc_start: 0.7359 (pm20) cc_final: 0.6822 (pm20) REVERT: c 126 ARG cc_start: 0.7687 (mpp-170) cc_final: 0.7408 (mpt180) REVERT: c 183 ASP cc_start: 0.7729 (t0) cc_final: 0.7271 (t0) REVERT: c 184 TYR cc_start: 0.8821 (t80) cc_final: 0.8613 (t80) REVERT: d 45 GLU cc_start: 0.7822 (tp30) cc_final: 0.7419 (tp30) REVERT: d 47 LEU cc_start: 0.8977 (tp) cc_final: 0.8746 (tp) REVERT: d 52 GLU cc_start: 0.7124 (tp30) cc_final: 0.6767 (tp30) REVERT: d 89 LEU cc_start: 0.8412 (mt) cc_final: 0.8013 (mt) REVERT: d 119 ASN cc_start: 0.7961 (m-40) cc_final: 0.6323 (t0) REVERT: d 167 GLN cc_start: 0.6872 (tt0) cc_final: 0.6549 (tm-30) REVERT: d 176 LEU cc_start: 0.8243 (mp) cc_final: 0.7979 (mp) REVERT: d 190 LEU cc_start: 0.8294 (pt) cc_final: 0.7563 (pp) REVERT: e 105 VAL cc_start: 0.8423 (t) cc_final: 0.8162 (p) REVERT: e 158 SER cc_start: 0.8604 (p) cc_final: 0.8400 (p) REVERT: f 92 ARG cc_start: 0.7282 (mtp180) cc_final: 0.6935 (mtm180) REVERT: g 33 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8250 (mttt) REVERT: g 93 PRO cc_start: 0.9168 (Cg_exo) cc_final: 0.8961 (Cg_endo) REVERT: h 41 LYS cc_start: 0.8290 (tttt) cc_final: 0.7931 (tttp) REVERT: h 103 VAL cc_start: 0.8800 (t) cc_final: 0.8565 (m) REVERT: h 107 SER cc_start: 0.8378 (t) cc_final: 0.8119 (m) REVERT: l 70 GLU cc_start: 0.6649 (pm20) cc_final: 0.6109 (pm20) REVERT: l 97 ILE cc_start: 0.8849 (mm) cc_final: 0.8529 (mt) REVERT: l 99 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8196 (mtp180) REVERT: m 109 THR cc_start: 0.7827 (m) cc_final: 0.7543 (p) REVERT: n 40 CYS cc_start: 0.6885 (p) cc_final: 0.6277 (p) REVERT: p 10 LEU cc_start: 0.8376 (pp) cc_final: 0.8054 (pp) REVERT: r 59 GLN cc_start: 0.7548 (mt0) cc_final: 0.7343 (mt0) REVERT: t 22 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8262 (tttt) REVERT: t 60 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7691 (mttt) REVERT: x 56 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8471 (ttpp) REVERT: x 72 ILE cc_start: 0.7388 (tt) cc_final: 0.6931 (tp) REVERT: x 93 MET cc_start: 0.6705 (mtt) cc_final: 0.6423 (mtt) REVERT: x 99 LYS cc_start: 0.6829 (mtmt) cc_final: 0.6528 (mmpt) REVERT: x 209 ILE cc_start: 0.8035 (mt) cc_final: 0.7802 (mt) REVERT: x 255 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7736 (tp40) REVERT: x 259 ASP cc_start: 0.7505 (p0) cc_final: 0.7201 (p0) REVERT: x 308 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7264 (tp30) REVERT: x 338 LYS cc_start: 0.7972 (tppp) cc_final: 0.7558 (ttpt) REVERT: x 364 PHE cc_start: 0.7944 (m-10) cc_final: 0.7515 (m-80) REVERT: x 449 ASN cc_start: 0.8043 (t0) cc_final: 0.7731 (t0) REVERT: x 467 ASP cc_start: 0.6199 (t0) cc_final: 0.5915 (t0) REVERT: x 557 ARG cc_start: 0.7472 (ppt170) cc_final: 0.7231 (ppt170) outliers start: 3 outliers final: 1 residues processed: 1312 average time/residue: 1.4687 time to fit residues: 3195.4842 Evaluate side-chains 972 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 970 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain S residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 20.0000 chunk 812 optimal weight: 9.9990 chunk 450 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 548 optimal weight: 5.9990 chunk 434 optimal weight: 2.9990 chunk 840 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 510 optimal weight: 2.9990 chunk 625 optimal weight: 1.9990 chunk 973 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS 1 22 ASN 1 49 GLN ** 8 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 231 ASN C 245 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN F 162 ASN G 144 GLN H 46 GLN J 71 HIS J 144 GLN J 147 GLN M 14 HIS O 36 HIS O 48 ASN P 28 HIS Q 11 HIS Q 44 ASN R 94 GLN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 ASN V 44 HIS ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 ASN W 12 ASN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 HIS d 66 GLN d 115 HIS ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 153 HIS ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 38 GLN i 65 HIS j 4 GLN j 70 HIS ** k 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN o 48 HIS o 51 HIS p 15 ASN q 70 GLN s 47 HIS s 52 HIS x 40 ASN x 58 ASN x 74 GLN x 88 ASN ** x 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 201 HIS x 319 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 414 GLN ** x 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 497 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 164814 Z= 0.237 Angle : 0.665 23.908 246731 Z= 0.339 Chirality : 0.038 0.268 31470 Planarity : 0.006 0.126 13363 Dihedral : 23.314 179.634 82920 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.07 % Rotamer: Outliers : 2.13 % Allowed : 9.95 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.09), residues: 6045 helix: -3.32 (0.09), residues: 1688 sheet: -1.75 (0.16), residues: 1006 loop : -2.53 (0.09), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 22 HIS 0.007 0.001 HIS q 46 PHE 0.024 0.002 PHE x 431 TYR 0.020 0.002 TYR l 38 ARG 0.007 0.001 ARG e 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1008 time to evaluate : 6.187 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: 4 22 ARG cc_start: 0.7567 (ptp-110) cc_final: 0.7000 (ptt180) REVERT: 8 58 MET cc_start: 0.6957 (tpt) cc_final: 0.6145 (tmm) REVERT: 8 181 ASP cc_start: 0.7316 (m-30) cc_final: 0.6626 (p0) REVERT: 8 200 LYS cc_start: 0.8132 (tptm) cc_final: 0.6687 (pttm) REVERT: 8 210 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6965 (mtmt) REVERT: C 130 ASN cc_start: 0.7748 (t0) cc_final: 0.7529 (t0) REVERT: C 179 SER cc_start: 0.8124 (p) cc_final: 0.7909 (p) REVERT: E 177 ASN cc_start: 0.7522 (p0) cc_final: 0.7145 (p0) REVERT: E 178 LEU cc_start: 0.8380 (mt) cc_final: 0.8131 (mt) REVERT: E 187 ASP cc_start: 0.8132 (p0) cc_final: 0.7796 (p0) REVERT: F 130 ASP cc_start: 0.8010 (p0) cc_final: 0.7743 (p0) REVERT: G 87 LYS cc_start: 0.7465 (tttt) cc_final: 0.7132 (mmmt) REVERT: G 131 LYS cc_start: 0.7114 (mttm) cc_final: 0.6890 (mttp) REVERT: G 139 LYS cc_start: 0.6231 (tttt) cc_final: 0.5961 (tttt) REVERT: G 153 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6343 (tpp80) REVERT: G 154 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7270 (ttm-80) REVERT: H 12 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8331 (tm) REVERT: J 129 GLU cc_start: 0.7612 (tp30) cc_final: 0.7340 (tp30) REVERT: K 88 LYS cc_start: 0.8597 (mttp) cc_final: 0.8370 (mttp) REVERT: K 90 ASP cc_start: 0.7684 (p0) cc_final: 0.7479 (p0) REVERT: L 18 ARG cc_start: 0.7902 (ttt-90) cc_final: 0.7655 (ttm-80) REVERT: M 120 ARG cc_start: 0.6558 (mtt-85) cc_final: 0.6212 (mtp-110) REVERT: O 34 VAL cc_start: 0.8297 (t) cc_final: 0.7709 (m) REVERT: O 60 SER cc_start: 0.8833 (m) cc_final: 0.8494 (t) REVERT: O 83 ILE cc_start: 0.7571 (tt) cc_final: 0.7369 (tp) REVERT: T 77 LYS cc_start: 0.8741 (ptmt) cc_final: 0.8460 (pttt) REVERT: U 103 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6303 (mmmt) REVERT: W 26 TYR cc_start: 0.8952 (m-80) cc_final: 0.8724 (m-10) REVERT: X 27 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8350 (ptm-80) REVERT: Y 63 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8011 (mt-10) REVERT: c 85 ARG cc_start: 0.7817 (tmm-80) cc_final: 0.7455 (tmm160) REVERT: c 97 GLN cc_start: 0.7235 (pm20) cc_final: 0.6651 (pm20) REVERT: c 170 GLU cc_start: 0.7639 (tp30) cc_final: 0.7340 (tp30) REVERT: d 45 GLU cc_start: 0.8036 (tp30) cc_final: 0.7569 (tp30) REVERT: d 52 GLU cc_start: 0.6977 (tp30) cc_final: 0.6680 (tp30) REVERT: d 89 LEU cc_start: 0.8436 (mt) cc_final: 0.7971 (mt) REVERT: d 119 ASN cc_start: 0.7913 (m-40) cc_final: 0.6177 (t0) REVERT: d 135 TYR cc_start: 0.7576 (m-10) cc_final: 0.7251 (m-80) REVERT: d 190 LEU cc_start: 0.8239 (pt) cc_final: 0.7381 (pp) REVERT: e 158 SER cc_start: 0.8498 (p) cc_final: 0.8293 (p) REVERT: f 92 ARG cc_start: 0.7369 (mtp180) cc_final: 0.7147 (mtm180) REVERT: g 29 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7336 (mmtt) REVERT: g 33 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8184 (mttt) REVERT: g 53 LYS cc_start: 0.7671 (mtpm) cc_final: 0.7377 (mttp) REVERT: h 27 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7440 (pt) REVERT: h 41 LYS cc_start: 0.8203 (tttt) cc_final: 0.7963 (tttp) REVERT: i 144 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7269 (tttt) REVERT: j 67 MET cc_start: 0.7602 (tmm) cc_final: 0.7293 (tmm) REVERT: l 70 GLU cc_start: 0.6892 (pm20) cc_final: 0.6371 (pm20) REVERT: l 97 ILE cc_start: 0.8720 (mm) cc_final: 0.8429 (mt) REVERT: l 99 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: m 109 THR cc_start: 0.7866 (m) cc_final: 0.7626 (p) REVERT: p 10 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8078 (pp) REVERT: q 42 LYS cc_start: 0.5516 (mmmm) cc_final: 0.4910 (mppt) REVERT: q 113 LEU cc_start: 0.8439 (mt) cc_final: 0.8141 (mp) REVERT: r 49 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7982 (mtt90) REVERT: s 74 PHE cc_start: 0.8518 (m-80) cc_final: 0.8245 (m-80) REVERT: t 60 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7610 (mttm) REVERT: x 56 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8409 (ttpp) REVERT: x 93 MET cc_start: 0.6726 (mtt) cc_final: 0.6478 (mtt) REVERT: x 126 GLN cc_start: 0.7747 (mt0) cc_final: 0.7317 (pt0) REVERT: x 138 ASP cc_start: 0.4705 (m-30) cc_final: 0.4290 (t70) REVERT: x 146 ASP cc_start: 0.7620 (t70) cc_final: 0.7140 (t0) REVERT: x 196 GLN cc_start: 0.7956 (tt0) cc_final: 0.7736 (tp40) REVERT: x 224 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7106 (mt-10) REVERT: x 233 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.7079 (mtp85) REVERT: x 255 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7719 (tp40) REVERT: x 258 LYS cc_start: 0.8660 (tttp) cc_final: 0.8041 (ttpp) REVERT: x 308 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7379 (tp30) REVERT: x 379 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7405 (mtmt) REVERT: x 389 VAL cc_start: 0.4304 (OUTLIER) cc_final: 0.3991 (p) REVERT: x 467 ASP cc_start: 0.6125 (t0) cc_final: 0.5793 (t0) REVERT: x 557 ARG cc_start: 0.7107 (ppt170) cc_final: 0.6899 (ppt170) outliers start: 107 outliers final: 60 residues processed: 1060 average time/residue: 1.3674 time to fit residues: 2474.0154 Evaluate side-chains 1015 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 949 time to evaluate : 6.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 145 MET Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 158 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 3.9990 chunk 302 optimal weight: 20.0000 chunk 810 optimal weight: 10.0000 chunk 662 optimal weight: 50.0000 chunk 268 optimal weight: 8.9990 chunk 975 optimal weight: 7.9990 chunk 1053 optimal weight: 0.0040 chunk 868 optimal weight: 0.5980 chunk 967 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 overall best weight: 2.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 8 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN Q 44 ASN ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 ASN h 42 ASN j 47 ASN k 79 ASN ** k 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN p 57 GLN x 319 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 164814 Z= 0.216 Angle : 0.593 21.758 246731 Z= 0.304 Chirality : 0.035 0.241 31470 Planarity : 0.005 0.118 13363 Dihedral : 23.135 179.524 82919 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 2.89 % Allowed : 11.62 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.23 (0.10), residues: 6045 helix: -2.36 (0.11), residues: 1728 sheet: -1.46 (0.16), residues: 1015 loop : -2.26 (0.10), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP k 54 HIS 0.009 0.001 HIS 8 67 PHE 0.023 0.002 PHE P 6 TYR 0.022 0.002 TYR T 73 ARG 0.016 0.001 ARG c 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 972 time to evaluate : 6.153 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: 1 10 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8201 (mtmt) REVERT: 1 52 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7661 (mtp180) REVERT: 4 22 ARG cc_start: 0.7571 (ptp-110) cc_final: 0.6967 (ptt180) REVERT: 8 58 MET cc_start: 0.6940 (tpt) cc_final: 0.6011 (tmm) REVERT: 8 181 ASP cc_start: 0.7283 (m-30) cc_final: 0.6676 (p0) REVERT: 8 200 LYS cc_start: 0.8150 (tptm) cc_final: 0.6696 (pttm) REVERT: 8 210 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6922 (mtmt) REVERT: C 179 SER cc_start: 0.7973 (p) cc_final: 0.7677 (p) REVERT: E 10 LYS cc_start: 0.7671 (mmmm) cc_final: 0.7249 (mtpt) REVERT: E 177 ASN cc_start: 0.7626 (p0) cc_final: 0.7277 (p0) REVERT: E 178 LEU cc_start: 0.8372 (mt) cc_final: 0.8136 (mt) REVERT: E 187 ASP cc_start: 0.8139 (p0) cc_final: 0.7815 (p0) REVERT: F 103 MET cc_start: 0.7806 (ttp) cc_final: 0.7569 (ttp) REVERT: F 130 ASP cc_start: 0.8050 (p0) cc_final: 0.7802 (p0) REVERT: F 160 ASP cc_start: 0.6085 (OUTLIER) cc_final: 0.5766 (p0) REVERT: G 87 LYS cc_start: 0.7506 (tttt) cc_final: 0.7167 (mmmt) REVERT: G 153 ARG cc_start: 0.7445 (mmm160) cc_final: 0.6344 (tpp80) REVERT: H 12 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8293 (tm) REVERT: J 129 GLU cc_start: 0.7630 (tp30) cc_final: 0.7359 (tp30) REVERT: K 104 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: L 18 ARG cc_start: 0.7946 (ttt-90) cc_final: 0.7744 (ttm-80) REVERT: L 85 LEU cc_start: 0.8346 (mt) cc_final: 0.8032 (mt) REVERT: L 100 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8321 (mmmt) REVERT: M 120 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.6151 (mtp-110) REVERT: O 34 VAL cc_start: 0.8294 (t) cc_final: 0.7641 (m) REVERT: O 60 SER cc_start: 0.8856 (m) cc_final: 0.8511 (t) REVERT: S 18 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8165 (mtm110) REVERT: T 77 LYS cc_start: 0.8751 (ptmt) cc_final: 0.8543 (pttt) REVERT: U 103 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6238 (mmmt) REVERT: W 26 TYR cc_start: 0.8955 (m-80) cc_final: 0.8747 (m-10) REVERT: c 97 GLN cc_start: 0.7126 (pm20) cc_final: 0.6674 (pm20) REVERT: c 133 MET cc_start: 0.8397 (mtm) cc_final: 0.7992 (mtt) REVERT: d 45 GLU cc_start: 0.8089 (tp30) cc_final: 0.7641 (tp30) REVERT: d 52 GLU cc_start: 0.6870 (tp30) cc_final: 0.6610 (tp30) REVERT: d 89 LEU cc_start: 0.8472 (mt) cc_final: 0.7974 (mt) REVERT: d 119 ASN cc_start: 0.8016 (m-40) cc_final: 0.6237 (t0) REVERT: d 190 LEU cc_start: 0.8274 (pt) cc_final: 0.7429 (pp) REVERT: e 158 SER cc_start: 0.8479 (p) cc_final: 0.8268 (p) REVERT: f 92 ARG cc_start: 0.7406 (mtp180) cc_final: 0.7190 (mtm180) REVERT: g 29 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7413 (mmtt) REVERT: g 53 LYS cc_start: 0.7679 (mtpm) cc_final: 0.7275 (mttp) REVERT: h 27 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7426 (pt) REVERT: j 67 MET cc_start: 0.7564 (tmm) cc_final: 0.7235 (tmm) REVERT: k 51 VAL cc_start: 0.8829 (t) cc_final: 0.8613 (m) REVERT: l 70 GLU cc_start: 0.6763 (pm20) cc_final: 0.6257 (pm20) REVERT: l 97 ILE cc_start: 0.8794 (mm) cc_final: 0.8528 (mt) REVERT: l 99 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8431 (mmm-85) REVERT: m 109 THR cc_start: 0.7898 (m) cc_final: 0.7679 (p) REVERT: n 26 LYS cc_start: 0.7740 (tttm) cc_final: 0.7209 (ttmt) REVERT: p 10 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8040 (pp) REVERT: q 42 LYS cc_start: 0.5515 (mmmm) cc_final: 0.5068 (mppt) REVERT: s 74 PHE cc_start: 0.8455 (m-80) cc_final: 0.8166 (m-80) REVERT: t 5 LYS cc_start: 0.8995 (tppp) cc_final: 0.8587 (ttpt) REVERT: t 46 LYS cc_start: 0.6986 (mtpp) cc_final: 0.6599 (ttmt) REVERT: t 60 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7503 (mttp) REVERT: x 56 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8420 (ttpp) REVERT: x 83 LYS cc_start: 0.7698 (tppt) cc_final: 0.7479 (tppt) REVERT: x 93 MET cc_start: 0.6762 (mtt) cc_final: 0.6525 (mtt) REVERT: x 146 ASP cc_start: 0.7720 (t70) cc_final: 0.7256 (t0) REVERT: x 196 GLN cc_start: 0.7778 (tt0) cc_final: 0.7574 (tt0) REVERT: x 209 ILE cc_start: 0.7908 (mt) cc_final: 0.7625 (mt) REVERT: x 224 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6994 (mt-10) REVERT: x 233 ARG cc_start: 0.7165 (mmm-85) cc_final: 0.6772 (mtp85) REVERT: x 258 LYS cc_start: 0.8410 (tttp) cc_final: 0.8111 (ttpp) REVERT: x 308 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7363 (tp30) REVERT: x 379 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7320 (mtmt) REVERT: x 389 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.3952 (p) REVERT: x 400 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7867 (mtmm) REVERT: x 447 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7555 (mm-30) REVERT: x 467 ASP cc_start: 0.6158 (t0) cc_final: 0.5811 (t0) REVERT: x 534 GLU cc_start: 0.7946 (mp0) cc_final: 0.7743 (mp0) REVERT: x 557 ARG cc_start: 0.7108 (ppt170) cc_final: 0.6906 (ppt170) outliers start: 145 outliers final: 95 residues processed: 1049 average time/residue: 1.3587 time to fit residues: 2443.3852 Evaluate side-chains 1038 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 936 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 171 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 158 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 0.9990 chunk 733 optimal weight: 8.9990 chunk 506 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 465 optimal weight: 0.7980 chunk 654 optimal weight: 3.9990 chunk 978 optimal weight: 20.0000 chunk 1036 optimal weight: 10.0000 chunk 511 optimal weight: 1.9990 chunk 927 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 144 GLN P 2 ASN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN h 35 ASN j 47 ASN k 59 HIS k 111 GLN x 88 ASN x 126 GLN x 319 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 164814 Z= 0.227 Angle : 0.588 19.340 246731 Z= 0.300 Chirality : 0.035 0.247 31470 Planarity : 0.005 0.117 13363 Dihedral : 23.056 179.590 82919 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 3.31 % Allowed : 13.28 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.79 (0.10), residues: 6045 helix: -1.82 (0.12), residues: 1744 sheet: -1.26 (0.16), residues: 1017 loop : -2.07 (0.10), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 22 HIS 0.006 0.001 HIS G 66 PHE 0.025 0.002 PHE P 6 TYR 0.018 0.002 TYR Q 47 ARG 0.012 0.001 ARG f 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 951 time to evaluate : 6.541 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: 4 22 ARG cc_start: 0.7594 (ptp-110) cc_final: 0.6979 (ptt180) REVERT: 8 58 MET cc_start: 0.7015 (tpt) cc_final: 0.5995 (tmm) REVERT: 8 181 ASP cc_start: 0.7201 (m-30) cc_final: 0.6571 (p0) REVERT: 8 183 LYS cc_start: 0.8191 (tptp) cc_final: 0.7903 (tptp) REVERT: 8 200 LYS cc_start: 0.8239 (tptm) cc_final: 0.6756 (pttm) REVERT: 8 210 LYS cc_start: 0.7272 (mtmt) cc_final: 0.6899 (mtmt) REVERT: C 35 ARG cc_start: 0.7383 (mmt-90) cc_final: 0.7065 (mmt-90) REVERT: C 179 SER cc_start: 0.8011 (p) cc_final: 0.7699 (p) REVERT: C 270 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8242 (ttp80) REVERT: E 10 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7040 (mmmm) REVERT: E 177 ASN cc_start: 0.7659 (p0) cc_final: 0.7341 (p0) REVERT: E 187 ASP cc_start: 0.8111 (p0) cc_final: 0.7807 (p0) REVERT: F 103 MET cc_start: 0.7760 (ttp) cc_final: 0.7454 (ttp) REVERT: F 130 ASP cc_start: 0.8043 (p0) cc_final: 0.7816 (p0) REVERT: F 160 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5956 (p0) REVERT: G 87 LYS cc_start: 0.7528 (tttt) cc_final: 0.7186 (mmtt) REVERT: G 154 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7402 (ttm-80) REVERT: G 171 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7075 (tpp80) REVERT: H 12 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8310 (tm) REVERT: J 129 GLU cc_start: 0.7645 (tp30) cc_final: 0.7376 (tp30) REVERT: K 104 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: L 85 LEU cc_start: 0.8199 (mt) cc_final: 0.7907 (mt) REVERT: O 34 VAL cc_start: 0.8313 (t) cc_final: 0.7743 (m) REVERT: O 60 SER cc_start: 0.8861 (m) cc_final: 0.8538 (t) REVERT: P 29 VAL cc_start: 0.8264 (t) cc_final: 0.7845 (m) REVERT: P 93 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6831 (mtt-85) REVERT: S 18 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8145 (mtm110) REVERT: T 73 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: U 103 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6162 (mmmt) REVERT: W 26 TYR cc_start: 0.8943 (m-80) cc_final: 0.8724 (m-10) REVERT: c 51 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7521 (mp) REVERT: c 97 GLN cc_start: 0.7112 (pm20) cc_final: 0.6714 (pm20) REVERT: c 133 MET cc_start: 0.8400 (mtm) cc_final: 0.8102 (mtp) REVERT: d 45 GLU cc_start: 0.8312 (tp30) cc_final: 0.7854 (tp30) REVERT: d 52 GLU cc_start: 0.6807 (tp30) cc_final: 0.6569 (tp30) REVERT: d 85 LEU cc_start: 0.7345 (tp) cc_final: 0.7005 (tt) REVERT: d 89 LEU cc_start: 0.8513 (mt) cc_final: 0.7998 (mt) REVERT: d 90 GLU cc_start: 0.8713 (tp30) cc_final: 0.8202 (tp30) REVERT: d 190 LEU cc_start: 0.8270 (pt) cc_final: 0.7438 (pp) REVERT: e 158 SER cc_start: 0.8565 (p) cc_final: 0.8365 (p) REVERT: e 179 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6766 (pt0) REVERT: g 29 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7344 (mmtt) REVERT: g 91 VAL cc_start: 0.8857 (t) cc_final: 0.8541 (m) REVERT: g 120 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7522 (mt) REVERT: h 27 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7449 (pt) REVERT: h 108 THR cc_start: 0.8817 (p) cc_final: 0.8562 (t) REVERT: j 67 MET cc_start: 0.7527 (tmm) cc_final: 0.7178 (tmm) REVERT: k 51 VAL cc_start: 0.8722 (t) cc_final: 0.8465 (m) REVERT: l 70 GLU cc_start: 0.6735 (pm20) cc_final: 0.6223 (pm20) REVERT: l 97 ILE cc_start: 0.8804 (mm) cc_final: 0.8510 (mt) REVERT: l 99 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8448 (mmm-85) REVERT: n 19 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7519 (mmm-85) REVERT: n 26 LYS cc_start: 0.7649 (tttm) cc_final: 0.7409 (ttmm) REVERT: p 10 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8050 (pp) REVERT: q 42 LYS cc_start: 0.5615 (mmmm) cc_final: 0.5260 (mppt) REVERT: q 70 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: s 74 PHE cc_start: 0.8471 (m-80) cc_final: 0.8185 (m-80) REVERT: t 5 LYS cc_start: 0.9025 (tppp) cc_final: 0.8657 (ttpt) REVERT: t 46 LYS cc_start: 0.6926 (mtpp) cc_final: 0.6554 (ttmt) REVERT: t 57 LYS cc_start: 0.7424 (mttp) cc_final: 0.6835 (mmmt) REVERT: t 60 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7592 (mttm) REVERT: x 56 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8466 (ttpp) REVERT: x 83 LYS cc_start: 0.7586 (tppt) cc_final: 0.7282 (tppt) REVERT: x 146 ASP cc_start: 0.7735 (t70) cc_final: 0.7290 (t0) REVERT: x 196 GLN cc_start: 0.7727 (tt0) cc_final: 0.7524 (tt0) REVERT: x 209 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7707 (mt) REVERT: x 210 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6916 (mp) REVERT: x 224 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7081 (mt-10) REVERT: x 233 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6653 (mtp85) REVERT: x 308 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7389 (tp30) REVERT: x 343 SER cc_start: 0.8793 (t) cc_final: 0.8477 (p) REVERT: x 356 ASN cc_start: 0.7070 (m110) cc_final: 0.6837 (m110) REVERT: x 379 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7318 (mtmt) REVERT: x 389 VAL cc_start: 0.4381 (OUTLIER) cc_final: 0.4116 (p) REVERT: x 393 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7496 (mtt180) REVERT: x 400 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: x 447 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7519 (mm-30) REVERT: x 467 ASP cc_start: 0.6096 (t0) cc_final: 0.5755 (t0) outliers start: 166 outliers final: 116 residues processed: 1039 average time/residue: 1.3596 time to fit residues: 2432.8897 Evaluate side-chains 1053 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 921 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 145 VAL Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 20 LYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 70 GLN Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 158 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 495 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 8.9990 chunk 588 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 771 optimal weight: 20.0000 chunk 427 optimal weight: 3.9990 chunk 884 optimal weight: 10.0000 chunk 716 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 529 optimal weight: 2.9990 chunk 930 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN 8 67 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 114 HIS ** k 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 ASN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 164814 Z= 0.294 Angle : 0.625 19.053 246731 Z= 0.315 Chirality : 0.037 0.282 31470 Planarity : 0.005 0.117 13363 Dihedral : 23.037 179.364 82919 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 3.69 % Allowed : 13.92 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.10), residues: 6045 helix: -1.59 (0.12), residues: 1738 sheet: -1.11 (0.16), residues: 1008 loop : -2.02 (0.10), residues: 3299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 22 HIS 0.006 0.001 HIS N 54 PHE 0.028 0.002 PHE i 85 TYR 0.020 0.002 TYR Q 47 ARG 0.011 0.001 ARG U 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 954 time to evaluate : 6.210 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: 4 22 ARG cc_start: 0.7614 (ptp-110) cc_final: 0.6972 (ptt180) REVERT: 8 58 MET cc_start: 0.7007 (tpt) cc_final: 0.6697 (tpp) REVERT: 8 181 ASP cc_start: 0.7193 (m-30) cc_final: 0.6577 (p0) REVERT: 8 210 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6911 (mtmt) REVERT: C 35 ARG cc_start: 0.7369 (mmt-90) cc_final: 0.7081 (mmt-90) REVERT: C 130 ASN cc_start: 0.7876 (t0) cc_final: 0.7671 (t0) REVERT: C 179 SER cc_start: 0.8053 (p) cc_final: 0.7768 (p) REVERT: E 177 ASN cc_start: 0.7761 (p0) cc_final: 0.7406 (p0) REVERT: E 187 ASP cc_start: 0.8104 (p0) cc_final: 0.7805 (p0) REVERT: F 103 MET cc_start: 0.7747 (ttp) cc_final: 0.7413 (ttp) REVERT: G 87 LYS cc_start: 0.7483 (tttt) cc_final: 0.7152 (mmtt) REVERT: G 156 ASP cc_start: 0.7686 (t0) cc_final: 0.7349 (t0) REVERT: G 159 LYS cc_start: 0.8492 (mmmm) cc_final: 0.7933 (mmtp) REVERT: H 12 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8318 (tm) REVERT: J 129 GLU cc_start: 0.7640 (tp30) cc_final: 0.7358 (tp30) REVERT: K 92 ASP cc_start: 0.7284 (m-30) cc_final: 0.6889 (m-30) REVERT: K 104 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7794 (ttm-80) REVERT: O 34 VAL cc_start: 0.8323 (t) cc_final: 0.7744 (m) REVERT: O 60 SER cc_start: 0.8898 (m) cc_final: 0.8589 (t) REVERT: P 29 VAL cc_start: 0.8336 (t) cc_final: 0.7941 (m) REVERT: P 93 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6900 (mtt-85) REVERT: S 18 ARG cc_start: 0.8412 (mtp-110) cc_final: 0.8145 (mtm110) REVERT: S 88 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: U 103 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6176 (mmmt) REVERT: W 26 TYR cc_start: 0.8960 (m-80) cc_final: 0.8758 (m-10) REVERT: c 51 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7499 (mp) REVERT: c 97 GLN cc_start: 0.7185 (pm20) cc_final: 0.6723 (pm20) REVERT: c 170 GLU cc_start: 0.7620 (tp30) cc_final: 0.7293 (tm-30) REVERT: d 45 GLU cc_start: 0.8385 (tp30) cc_final: 0.7953 (tp30) REVERT: d 52 GLU cc_start: 0.6615 (tp30) cc_final: 0.6390 (tp30) REVERT: d 89 LEU cc_start: 0.8523 (mt) cc_final: 0.8080 (mt) REVERT: d 190 LEU cc_start: 0.8294 (pt) cc_final: 0.7395 (pp) REVERT: e 179 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: f 7 MET cc_start: 0.7300 (ttm) cc_final: 0.7072 (ttm) REVERT: f 45 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8672 (mmtt) REVERT: g 29 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7388 (mmtt) REVERT: g 91 VAL cc_start: 0.8854 (t) cc_final: 0.8527 (m) REVERT: g 120 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7591 (mt) REVERT: h 27 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7545 (pt) REVERT: h 103 VAL cc_start: 0.8651 (t) cc_final: 0.8247 (m) REVERT: h 108 THR cc_start: 0.8784 (p) cc_final: 0.8559 (t) REVERT: i 124 PHE cc_start: 0.5454 (m-80) cc_final: 0.4940 (m-80) REVERT: j 67 MET cc_start: 0.7584 (tmm) cc_final: 0.7241 (tmm) REVERT: l 70 GLU cc_start: 0.6691 (pm20) cc_final: 0.6164 (pm20) REVERT: l 97 ILE cc_start: 0.8840 (mm) cc_final: 0.8552 (mm) REVERT: l 99 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.8426 (mmm-85) REVERT: n 19 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7497 (mmm-85) REVERT: n 26 LYS cc_start: 0.7607 (tttm) cc_final: 0.7385 (ttmm) REVERT: p 10 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8084 (pp) REVERT: q 42 LYS cc_start: 0.5593 (mmmm) cc_final: 0.5305 (mppt) REVERT: r 49 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7787 (mtt90) REVERT: r 61 GLN cc_start: 0.7952 (tp40) cc_final: 0.6909 (tm-30) REVERT: s 74 PHE cc_start: 0.8508 (m-80) cc_final: 0.8197 (m-80) REVERT: t 5 LYS cc_start: 0.9034 (tppp) cc_final: 0.8685 (ttpt) REVERT: t 46 LYS cc_start: 0.6986 (mtpp) cc_final: 0.6630 (ttmt) REVERT: t 57 LYS cc_start: 0.7495 (mttp) cc_final: 0.6845 (mmmt) REVERT: t 60 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7594 (mttp) REVERT: x 51 MET cc_start: 0.8634 (ttm) cc_final: 0.8421 (mtp) REVERT: x 56 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8424 (ttpp) REVERT: x 83 LYS cc_start: 0.7498 (tppt) cc_final: 0.7172 (tppt) REVERT: x 91 GLU cc_start: 0.3017 (OUTLIER) cc_final: 0.2626 (mp0) REVERT: x 146 ASP cc_start: 0.7666 (t70) cc_final: 0.7147 (t0) REVERT: x 196 GLN cc_start: 0.7741 (tt0) cc_final: 0.7538 (tp40) REVERT: x 224 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7069 (mt-10) REVERT: x 233 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6758 (mtp85) REVERT: x 308 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7326 (tp30) REVERT: x 343 SER cc_start: 0.8775 (t) cc_final: 0.8453 (p) REVERT: x 372 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7679 (p) REVERT: x 379 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7437 (mtmt) REVERT: x 389 VAL cc_start: 0.4428 (OUTLIER) cc_final: 0.4194 (p) REVERT: x 400 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: x 447 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7493 (mm-30) REVERT: x 467 ASP cc_start: 0.6394 (t0) cc_final: 0.6150 (t0) outliers start: 185 outliers final: 146 residues processed: 1047 average time/residue: 1.3218 time to fit residues: 2388.2829 Evaluate side-chains 1091 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 931 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 88 GLN Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 93 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 91 GLU Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 126 GLN Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 158 THR Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 215 ASP Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 344 LEU Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 506 CYS Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 10.0000 chunk 933 optimal weight: 4.9990 chunk 204 optimal weight: 70.0000 chunk 608 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 1037 optimal weight: 20.0000 chunk 861 optimal weight: 9.9990 chunk 480 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 544 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN 8 172 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 144 GLN ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN d 115 HIS k 111 GLN x 508 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 164814 Z= 0.338 Angle : 0.654 18.839 246731 Z= 0.328 Chirality : 0.038 0.293 31470 Planarity : 0.005 0.117 13363 Dihedral : 23.036 179.340 82919 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 4.07 % Allowed : 14.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 6045 helix: -1.49 (0.12), residues: 1750 sheet: -1.10 (0.16), residues: 1009 loop : -2.01 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 22 HIS 0.008 0.002 HIS d 115 PHE 0.026 0.002 PHE P 6 TYR 0.022 0.002 TYR Q 47 ARG 0.010 0.001 ARG U 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 956 time to evaluate : 6.240 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: 4 22 ARG cc_start: 0.7624 (ptp-110) cc_final: 0.6982 (ptt180) REVERT: 8 58 MET cc_start: 0.6963 (tpt) cc_final: 0.5755 (tmm) REVERT: 8 181 ASP cc_start: 0.7167 (m-30) cc_final: 0.6530 (p0) REVERT: 8 210 LYS cc_start: 0.7219 (mtmt) cc_final: 0.6854 (mtmt) REVERT: 8 229 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.6053 (m) REVERT: C 130 ASN cc_start: 0.7965 (t0) cc_final: 0.7758 (t0) REVERT: C 179 SER cc_start: 0.8092 (p) cc_final: 0.7815 (p) REVERT: E 177 ASN cc_start: 0.7799 (p0) cc_final: 0.7433 (p0) REVERT: E 187 ASP cc_start: 0.8100 (p0) cc_final: 0.7797 (p0) REVERT: F 103 MET cc_start: 0.7795 (ttp) cc_final: 0.7437 (ttp) REVERT: G 87 LYS cc_start: 0.7467 (tttt) cc_final: 0.7123 (mmtt) REVERT: G 154 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7483 (ttm-80) REVERT: G 156 ASP cc_start: 0.7741 (t0) cc_final: 0.7386 (t0) REVERT: H 12 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8318 (tm) REVERT: J 129 GLU cc_start: 0.7634 (tp30) cc_final: 0.7336 (tp30) REVERT: K 88 LYS cc_start: 0.8668 (mttp) cc_final: 0.8432 (mtmm) REVERT: K 92 ASP cc_start: 0.7291 (m-30) cc_final: 0.6954 (m-30) REVERT: K 104 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7828 (ttm-80) REVERT: O 34 VAL cc_start: 0.8312 (t) cc_final: 0.7751 (m) REVERT: O 60 SER cc_start: 0.8896 (m) cc_final: 0.8586 (t) REVERT: P 29 VAL cc_start: 0.8419 (t) cc_final: 0.7995 (m) REVERT: P 93 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6948 (mtt-85) REVERT: S 18 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.8162 (mtm110) REVERT: S 88 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: c 51 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7506 (mp) REVERT: c 97 GLN cc_start: 0.7224 (pm20) cc_final: 0.6736 (pm20) REVERT: c 133 MET cc_start: 0.8461 (mtm) cc_final: 0.8133 (mtp) REVERT: d 45 GLU cc_start: 0.8443 (tp30) cc_final: 0.8004 (tp30) REVERT: d 89 LEU cc_start: 0.8496 (mt) cc_final: 0.8048 (mt) REVERT: e 179 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: g 29 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7462 (mmtt) REVERT: g 91 VAL cc_start: 0.8857 (t) cc_final: 0.8518 (m) REVERT: g 120 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7584 (mt) REVERT: g 136 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7736 (tttp) REVERT: h 27 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7577 (pt) REVERT: h 103 VAL cc_start: 0.8693 (t) cc_final: 0.8284 (m) REVERT: h 108 THR cc_start: 0.8802 (p) cc_final: 0.8589 (t) REVERT: j 67 MET cc_start: 0.7592 (tmm) cc_final: 0.7252 (tmm) REVERT: l 70 GLU cc_start: 0.6730 (pm20) cc_final: 0.6173 (pm20) REVERT: l 97 ILE cc_start: 0.8834 (mm) cc_final: 0.8571 (mm) REVERT: m 15 MET cc_start: 0.6714 (tpp) cc_final: 0.5551 (mmm) REVERT: m 111 LYS cc_start: 0.7501 (mtmm) cc_final: 0.7074 (mtmm) REVERT: n 19 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7493 (mmm-85) REVERT: n 26 LYS cc_start: 0.7622 (tttm) cc_final: 0.7394 (ttmm) REVERT: p 10 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8073 (pp) REVERT: q 42 LYS cc_start: 0.5592 (mmmm) cc_final: 0.5338 (mppt) REVERT: q 70 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: r 49 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7963 (mtt90) REVERT: r 61 GLN cc_start: 0.8022 (tp40) cc_final: 0.6896 (tm-30) REVERT: s 74 PHE cc_start: 0.8537 (m-80) cc_final: 0.8212 (m-80) REVERT: t 5 LYS cc_start: 0.9071 (tppp) cc_final: 0.8723 (ttpt) REVERT: t 46 LYS cc_start: 0.7033 (mtpp) cc_final: 0.6691 (ttmt) REVERT: t 57 LYS cc_start: 0.7385 (mttp) cc_final: 0.6804 (mmmt) REVERT: t 60 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7657 (mttm) REVERT: x 34 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7948 (mm) REVERT: x 56 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8342 (ttpp) REVERT: x 83 LYS cc_start: 0.7445 (tppt) cc_final: 0.7101 (tppt) REVERT: x 91 GLU cc_start: 0.3091 (OUTLIER) cc_final: 0.2711 (mp0) REVERT: x 126 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: x 196 GLN cc_start: 0.7712 (tt0) cc_final: 0.7511 (tp40) REVERT: x 233 ARG cc_start: 0.7126 (mmm-85) cc_final: 0.6734 (mtp85) REVERT: x 308 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7353 (tp30) REVERT: x 343 SER cc_start: 0.8784 (t) cc_final: 0.8448 (p) REVERT: x 356 ASN cc_start: 0.7106 (m110) cc_final: 0.6828 (m110) REVERT: x 364 PHE cc_start: 0.7734 (m-10) cc_final: 0.7469 (m-10) REVERT: x 372 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7675 (p) REVERT: x 379 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7508 (mtmt) REVERT: x 389 VAL cc_start: 0.4465 (OUTLIER) cc_final: 0.4229 (p) REVERT: x 393 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7661 (mtm180) REVERT: x 400 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (mtmm) REVERT: x 447 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7482 (mm-30) REVERT: x 467 ASP cc_start: 0.6149 (t0) cc_final: 0.5947 (t0) outliers start: 204 outliers final: 157 residues processed: 1053 average time/residue: 1.3528 time to fit residues: 2457.4205 Evaluate side-chains 1127 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 952 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 229 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 88 GLN Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 70 GLN Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 93 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain q residue 132 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 91 GLU Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 126 GLN Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 175 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 215 ASP Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 273 VAL Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 506 CYS Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 590 optimal weight: 0.9990 chunk 757 optimal weight: 30.0000 chunk 586 optimal weight: 2.9990 chunk 873 optimal weight: 10.0000 chunk 579 optimal weight: 1.9990 chunk 1033 optimal weight: 10.0000 chunk 646 optimal weight: 0.8980 chunk 629 optimal weight: 10.0000 chunk 477 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 69 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 144 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN X 37 HIS ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 87 HIS k 111 GLN x 289 GLN ** x 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 164814 Z= 0.187 Angle : 0.561 18.092 246731 Z= 0.287 Chirality : 0.033 0.298 31470 Planarity : 0.005 0.117 13363 Dihedral : 22.981 179.916 82919 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.60 % Rotamer: Outliers : 3.13 % Allowed : 15.73 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.10), residues: 6045 helix: -1.13 (0.12), residues: 1750 sheet: -0.98 (0.16), residues: 1015 loop : -1.89 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 201 HIS 0.005 0.001 HIS G 66 PHE 0.022 0.001 PHE P 6 TYR 0.018 0.001 TYR C 104 ARG 0.010 0.000 ARG c 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 964 time to evaluate : 6.160 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: 0 6 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8351 (mtt-85) REVERT: 4 22 ARG cc_start: 0.7552 (ptp-110) cc_final: 0.6927 (ptt180) REVERT: 8 58 MET cc_start: 0.6964 (tpt) cc_final: 0.6601 (tpp) REVERT: 8 181 ASP cc_start: 0.7202 (m-30) cc_final: 0.6567 (p0) REVERT: 8 210 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6845 (mtmt) REVERT: 8 229 THR cc_start: 0.6369 (OUTLIER) cc_final: 0.6017 (m) REVERT: C 130 ASN cc_start: 0.7875 (t0) cc_final: 0.7649 (t0) REVERT: C 179 SER cc_start: 0.8047 (p) cc_final: 0.7770 (p) REVERT: E 177 ASN cc_start: 0.7566 (p0) cc_final: 0.7362 (p0) REVERT: E 187 ASP cc_start: 0.8058 (p0) cc_final: 0.7779 (p0) REVERT: F 103 MET cc_start: 0.7643 (ttp) cc_final: 0.7275 (ttp) REVERT: F 130 ASP cc_start: 0.8107 (p0) cc_final: 0.7762 (p0) REVERT: G 87 LYS cc_start: 0.7570 (tttt) cc_final: 0.7245 (mmtt) REVERT: G 154 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7507 (ttm-80) REVERT: G 156 ASP cc_start: 0.7712 (t0) cc_final: 0.7351 (t0) REVERT: G 159 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7871 (mmtp) REVERT: G 176 LYS cc_start: 0.6282 (tttp) cc_final: 0.5175 (ttmt) REVERT: H 12 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8287 (tm) REVERT: J 129 GLU cc_start: 0.7625 (tp30) cc_final: 0.7329 (tp30) REVERT: K 88 LYS cc_start: 0.8596 (mttp) cc_final: 0.8327 (mtmm) REVERT: K 92 ASP cc_start: 0.7241 (m-30) cc_final: 0.6922 (m-30) REVERT: K 112 MET cc_start: 0.7723 (mmm) cc_final: 0.7390 (mmt) REVERT: L 85 LEU cc_start: 0.8183 (mt) cc_final: 0.7887 (mt) REVERT: O 34 VAL cc_start: 0.8244 (t) cc_final: 0.7669 (m) REVERT: O 60 SER cc_start: 0.8872 (m) cc_final: 0.8553 (t) REVERT: O 98 ASP cc_start: 0.8651 (t0) cc_final: 0.8254 (t0) REVERT: P 29 VAL cc_start: 0.8403 (t) cc_final: 0.8017 (m) REVERT: P 93 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6924 (mtt-85) REVERT: S 18 ARG cc_start: 0.8413 (mtp-110) cc_final: 0.8130 (mtm110) REVERT: U 2 LYS cc_start: 0.8784 (mttt) cc_final: 0.8467 (mttt) REVERT: W 41 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8237 (tpp-160) REVERT: c 51 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7444 (mp) REVERT: c 97 GLN cc_start: 0.7214 (pm20) cc_final: 0.6768 (pm20) REVERT: c 133 MET cc_start: 0.8526 (mtm) cc_final: 0.8206 (mtp) REVERT: c 141 MET cc_start: 0.7513 (tpp) cc_final: 0.7087 (mtp) REVERT: d 45 GLU cc_start: 0.8398 (tp30) cc_final: 0.7984 (tp30) REVERT: d 52 GLU cc_start: 0.6474 (tp30) cc_final: 0.6060 (tp30) REVERT: d 89 LEU cc_start: 0.8491 (mt) cc_final: 0.7912 (mt) REVERT: d 190 LEU cc_start: 0.7750 (pt) cc_final: 0.7408 (pp) REVERT: e 179 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: f 92 ARG cc_start: 0.6982 (mtm180) cc_final: 0.6717 (mtp180) REVERT: g 29 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7428 (mmtt) REVERT: g 120 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7571 (mt) REVERT: h 27 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7428 (pt) REVERT: h 108 THR cc_start: 0.8781 (p) cc_final: 0.8536 (t) REVERT: i 124 PHE cc_start: 0.5625 (m-80) cc_final: 0.5270 (m-80) REVERT: j 16 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6080 (pm20) REVERT: j 67 MET cc_start: 0.7560 (tmm) cc_final: 0.7210 (tmm) REVERT: k 51 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8421 (m) REVERT: l 70 GLU cc_start: 0.6615 (pm20) cc_final: 0.6126 (pm20) REVERT: l 97 ILE cc_start: 0.8812 (mm) cc_final: 0.8552 (mm) REVERT: n 19 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7376 (mmm-85) REVERT: n 26 LYS cc_start: 0.7588 (tttm) cc_final: 0.7369 (ttmm) REVERT: p 10 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8076 (pp) REVERT: q 70 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: q 81 MET cc_start: 0.7602 (ptm) cc_final: 0.7277 (ptt) REVERT: q 123 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7595 (ttmt) REVERT: r 49 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7705 (mtt90) REVERT: r 59 GLN cc_start: 0.7512 (mt0) cc_final: 0.7274 (mt0) REVERT: s 74 PHE cc_start: 0.8480 (m-80) cc_final: 0.8185 (m-80) REVERT: t 5 LYS cc_start: 0.9041 (tppp) cc_final: 0.8765 (ttpt) REVERT: t 46 LYS cc_start: 0.6874 (mtpp) cc_final: 0.6622 (ttmt) REVERT: t 57 LYS cc_start: 0.7318 (mttp) cc_final: 0.6749 (mmmt) REVERT: t 60 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7437 (mttp) REVERT: x 34 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7891 (mm) REVERT: x 56 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8366 (ttpp) REVERT: x 83 LYS cc_start: 0.7380 (tppt) cc_final: 0.7093 (tppt) REVERT: x 126 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: x 196 GLN cc_start: 0.7676 (tt0) cc_final: 0.7465 (tp40) REVERT: x 224 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7069 (mt-10) REVERT: x 233 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6669 (mtp-110) REVERT: x 308 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7296 (tp30) REVERT: x 343 SER cc_start: 0.8737 (t) cc_final: 0.8411 (p) REVERT: x 356 ASN cc_start: 0.6865 (m110) cc_final: 0.6562 (m110) REVERT: x 364 PHE cc_start: 0.7686 (m-10) cc_final: 0.7413 (m-10) REVERT: x 379 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7404 (mtmt) REVERT: x 389 VAL cc_start: 0.4367 (OUTLIER) cc_final: 0.4119 (p) REVERT: x 393 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7504 (mtt180) REVERT: x 400 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: x 447 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7511 (mm-30) REVERT: x 467 ASP cc_start: 0.6134 (t0) cc_final: 0.5860 (t0) outliers start: 157 outliers final: 114 residues processed: 1043 average time/residue: 1.4404 time to fit residues: 2595.2446 Evaluate side-chains 1076 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 946 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 229 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 100 ARG Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 70 GLN Chi-restraints excluded: chain q residue 93 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain q residue 132 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 126 GLN Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 344 LEU Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 0.9990 chunk 412 optimal weight: 8.9990 chunk 617 optimal weight: 0.9990 chunk 311 optimal weight: 10.0000 chunk 203 optimal weight: 60.0000 chunk 200 optimal weight: 8.9990 chunk 656 optimal weight: 8.9990 chunk 703 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 812 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 144 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN k 87 HIS ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 164814 Z= 0.266 Angle : 0.604 18.041 246731 Z= 0.305 Chirality : 0.036 0.302 31470 Planarity : 0.005 0.117 13363 Dihedral : 22.971 179.536 82919 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 3.55 % Allowed : 15.87 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.23 (0.10), residues: 6045 helix: -1.10 (0.12), residues: 1753 sheet: -0.96 (0.16), residues: 1019 loop : -1.87 (0.10), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.005 0.001 HIS S 112 PHE 0.023 0.002 PHE P 6 TYR 0.019 0.001 TYR Q 47 ARG 0.010 0.001 ARG c 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 955 time to evaluate : 6.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 22 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.6945 (ptt180) REVERT: 8 181 ASP cc_start: 0.7181 (m-30) cc_final: 0.6549 (p0) REVERT: 8 210 LYS cc_start: 0.7199 (mtmt) cc_final: 0.6855 (mtmt) REVERT: 8 229 THR cc_start: 0.6379 (OUTLIER) cc_final: 0.6040 (m) REVERT: C 130 ASN cc_start: 0.7903 (t0) cc_final: 0.7668 (t0) REVERT: C 179 SER cc_start: 0.8073 (p) cc_final: 0.7810 (p) REVERT: E 177 ASN cc_start: 0.7827 (p0) cc_final: 0.7437 (p0) REVERT: E 187 ASP cc_start: 0.8053 (p0) cc_final: 0.7803 (p0) REVERT: F 103 MET cc_start: 0.7693 (ttp) cc_final: 0.7324 (ttp) REVERT: F 130 ASP cc_start: 0.8105 (p0) cc_final: 0.7823 (p0) REVERT: G 87 LYS cc_start: 0.7575 (tttt) cc_final: 0.7255 (mmtt) REVERT: G 156 ASP cc_start: 0.7731 (t0) cc_final: 0.7363 (t0) REVERT: G 159 LYS cc_start: 0.8499 (mmmm) cc_final: 0.7922 (mmtp) REVERT: G 176 LYS cc_start: 0.6269 (tttp) cc_final: 0.5195 (ttmt) REVERT: H 12 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8276 (tm) REVERT: J 129 GLU cc_start: 0.7625 (tp30) cc_final: 0.7319 (tp30) REVERT: K 88 LYS cc_start: 0.8616 (mttp) cc_final: 0.8353 (mtmm) REVERT: K 92 ASP cc_start: 0.7277 (m-30) cc_final: 0.6965 (m-30) REVERT: O 34 VAL cc_start: 0.8293 (t) cc_final: 0.7743 (m) REVERT: O 60 SER cc_start: 0.8902 (m) cc_final: 0.8589 (t) REVERT: O 98 ASP cc_start: 0.8678 (t0) cc_final: 0.8275 (t0) REVERT: P 29 VAL cc_start: 0.8428 (t) cc_final: 0.8033 (m) REVERT: P 48 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7821 (ttp-170) REVERT: P 65 TYR cc_start: 0.8487 (m-80) cc_final: 0.8180 (m-80) REVERT: P 93 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6981 (mtt-85) REVERT: U 2 LYS cc_start: 0.8833 (mttt) cc_final: 0.8461 (mttp) REVERT: c 51 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7486 (mp) REVERT: c 97 GLN cc_start: 0.7134 (pm20) cc_final: 0.6737 (pm20) REVERT: c 133 MET cc_start: 0.8525 (mtm) cc_final: 0.8207 (mtp) REVERT: c 141 MET cc_start: 0.7614 (tpp) cc_final: 0.7146 (mtp) REVERT: d 45 GLU cc_start: 0.8460 (tp30) cc_final: 0.8042 (tp30) REVERT: d 52 GLU cc_start: 0.6510 (tp30) cc_final: 0.6084 (tp30) REVERT: d 89 LEU cc_start: 0.8500 (mt) cc_final: 0.8113 (mt) REVERT: d 190 LEU cc_start: 0.7798 (pt) cc_final: 0.7371 (pp) REVERT: e 179 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6712 (pt0) REVERT: f 92 ARG cc_start: 0.6984 (mtm180) cc_final: 0.6708 (mtm180) REVERT: g 29 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7445 (mmtt) REVERT: g 120 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7608 (mt) REVERT: h 27 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (pt) REVERT: h 103 VAL cc_start: 0.8675 (t) cc_final: 0.8266 (m) REVERT: h 108 THR cc_start: 0.8784 (p) cc_final: 0.8553 (t) REVERT: i 124 PHE cc_start: 0.5578 (m-80) cc_final: 0.5294 (m-80) REVERT: j 16 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6060 (pm20) REVERT: j 67 MET cc_start: 0.7537 (tmm) cc_final: 0.7156 (tmm) REVERT: k 51 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (m) REVERT: k 111 GLN cc_start: 0.8379 (mm110) cc_final: 0.8139 (mm110) REVERT: l 70 GLU cc_start: 0.6636 (pm20) cc_final: 0.6122 (pm20) REVERT: l 97 ILE cc_start: 0.8827 (mm) cc_final: 0.8589 (mm) REVERT: m 111 LYS cc_start: 0.7520 (mtmm) cc_final: 0.7073 (mtmm) REVERT: n 19 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7441 (mmm-85) REVERT: n 26 LYS cc_start: 0.7606 (tttm) cc_final: 0.7230 (ttmt) REVERT: p 10 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8096 (pp) REVERT: q 70 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: q 81 MET cc_start: 0.7646 (ptm) cc_final: 0.7311 (ptt) REVERT: q 123 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7666 (ttmt) REVERT: r 49 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7722 (mtt90) REVERT: r 59 GLN cc_start: 0.7524 (mt0) cc_final: 0.7243 (mt0) REVERT: s 74 PHE cc_start: 0.8515 (m-80) cc_final: 0.8196 (m-80) REVERT: t 5 LYS cc_start: 0.9030 (tppp) cc_final: 0.8769 (ttpt) REVERT: t 46 LYS cc_start: 0.7006 (mtpp) cc_final: 0.6683 (ttmt) REVERT: t 57 LYS cc_start: 0.7326 (mttp) cc_final: 0.6728 (mmmt) REVERT: t 60 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7482 (mttp) REVERT: t 64 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7782 (tttt) REVERT: x 34 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mm) REVERT: x 56 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8296 (ttpp) REVERT: x 83 LYS cc_start: 0.7321 (tppt) cc_final: 0.7037 (tppt) REVERT: x 91 GLU cc_start: 0.3089 (OUTLIER) cc_final: 0.2599 (mp0) REVERT: x 196 GLN cc_start: 0.7692 (tt0) cc_final: 0.7487 (tp40) REVERT: x 224 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7097 (mt-10) REVERT: x 233 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6631 (mtp-110) REVERT: x 308 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7238 (tp30) REVERT: x 343 SER cc_start: 0.8757 (t) cc_final: 0.8402 (p) REVERT: x 356 ASN cc_start: 0.6991 (m110) cc_final: 0.6623 (m110) REVERT: x 364 PHE cc_start: 0.7709 (m-10) cc_final: 0.7439 (m-10) REVERT: x 379 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7509 (mtmt) REVERT: x 389 VAL cc_start: 0.4432 (OUTLIER) cc_final: 0.4205 (p) REVERT: x 400 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (mtmm) REVERT: x 447 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7412 (mm-30) REVERT: x 467 ASP cc_start: 0.6281 (t0) cc_final: 0.5982 (t0) REVERT: x 519 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6463 (mm-30) outliers start: 178 outliers final: 146 residues processed: 1041 average time/residue: 1.4604 time to fit residues: 2653.9237 Evaluate side-chains 1110 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 946 time to evaluate : 6.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 145 VAL Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 229 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 48 ARG Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 100 ARG Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 61 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 ARG Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 70 GLN Chi-restraints excluded: chain q residue 93 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain r residue 73 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 91 GLU Chi-restraints excluded: chain x residue 122 MET Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 175 LEU Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 344 LEU Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 400 LYS Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 483 ASN Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 519 GLU Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 5.9990 chunk 989 optimal weight: 7.9990 chunk 903 optimal weight: 0.9990 chunk 962 optimal weight: 0.8980 chunk 579 optimal weight: 9.9990 chunk 419 optimal weight: 0.9990 chunk 756 optimal weight: 60.0000 chunk 295 optimal weight: 6.9990 chunk 870 optimal weight: 3.9990 chunk 910 optimal weight: 7.9990 chunk 959 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN Y 31 ASN k 87 HIS r 61 GLN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 164814 Z= 0.154 Angle : 0.541 17.590 246731 Z= 0.277 Chirality : 0.032 0.319 31470 Planarity : 0.005 0.116 13363 Dihedral : 22.945 179.531 82919 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.17 % Allowed : 16.41 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.02 (0.10), residues: 6045 helix: -0.82 (0.13), residues: 1764 sheet: -0.88 (0.16), residues: 1019 loop : -1.80 (0.10), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 201 HIS 0.005 0.001 HIS G 66 PHE 0.022 0.001 PHE P 6 TYR 0.016 0.001 TYR C 104 ARG 0.011 0.000 ARG f 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 950 time to evaluate : 6.222 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: 1 10 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8208 (mtmt) REVERT: 4 22 ARG cc_start: 0.7548 (ptp-110) cc_final: 0.6890 (ptt180) REVERT: 8 181 ASP cc_start: 0.7163 (m-30) cc_final: 0.6547 (p0) REVERT: 8 210 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6903 (mtmt) REVERT: 8 229 THR cc_start: 0.6337 (OUTLIER) cc_final: 0.6026 (m) REVERT: C 130 ASN cc_start: 0.7885 (t0) cc_final: 0.7652 (t0) REVERT: C 179 SER cc_start: 0.8032 (p) cc_final: 0.7760 (p) REVERT: D 117 THR cc_start: 0.8646 (m) cc_final: 0.8358 (p) REVERT: E 187 ASP cc_start: 0.8020 (p0) cc_final: 0.7784 (p0) REVERT: F 103 MET cc_start: 0.7552 (ttp) cc_final: 0.7209 (ttp) REVERT: F 130 ASP cc_start: 0.8133 (p0) cc_final: 0.7907 (p0) REVERT: G 87 LYS cc_start: 0.7550 (tttt) cc_final: 0.7142 (mmtt) REVERT: G 156 ASP cc_start: 0.7716 (t0) cc_final: 0.7346 (t0) REVERT: G 159 LYS cc_start: 0.8508 (mmmm) cc_final: 0.7911 (mmtp) REVERT: H 12 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8261 (tm) REVERT: J 129 GLU cc_start: 0.7626 (tp30) cc_final: 0.7327 (tp30) REVERT: K 92 ASP cc_start: 0.7250 (m-30) cc_final: 0.6943 (m-30) REVERT: K 112 MET cc_start: 0.7691 (mmm) cc_final: 0.7337 (mmt) REVERT: O 34 VAL cc_start: 0.8235 (t) cc_final: 0.7669 (m) REVERT: O 60 SER cc_start: 0.8879 (m) cc_final: 0.8560 (t) REVERT: O 98 ASP cc_start: 0.8652 (t0) cc_final: 0.8260 (t0) REVERT: P 29 VAL cc_start: 0.8396 (t) cc_final: 0.8030 (m) REVERT: P 65 TYR cc_start: 0.8420 (m-80) cc_final: 0.8111 (m-80) REVERT: P 93 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: U 1 MET cc_start: 0.8097 (tpp) cc_final: 0.7664 (ttt) REVERT: U 2 LYS cc_start: 0.8932 (mttt) cc_final: 0.8586 (mttt) REVERT: Y 31 ASN cc_start: 0.7788 (m110) cc_final: 0.7469 (m-40) REVERT: c 51 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7425 (mp) REVERT: c 87 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7859 (ttp80) REVERT: c 97 GLN cc_start: 0.7122 (pm20) cc_final: 0.6755 (pm20) REVERT: c 133 MET cc_start: 0.8508 (mtm) cc_final: 0.8204 (mtp) REVERT: c 141 MET cc_start: 0.7557 (tpp) cc_final: 0.7122 (mtp) REVERT: d 45 GLU cc_start: 0.8416 (tp30) cc_final: 0.8009 (tp30) REVERT: d 52 GLU cc_start: 0.6508 (tp30) cc_final: 0.6056 (tp30) REVERT: d 89 LEU cc_start: 0.8503 (mt) cc_final: 0.8044 (mt) REVERT: d 186 ILE cc_start: 0.8764 (mm) cc_final: 0.8564 (mp) REVERT: d 190 LEU cc_start: 0.7784 (pt) cc_final: 0.7250 (pp) REVERT: e 179 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6696 (pt0) REVERT: f 92 ARG cc_start: 0.6929 (mtm180) cc_final: 0.6658 (mtm180) REVERT: g 29 LYS cc_start: 0.7619 (mmmt) cc_final: 0.7418 (mmtt) REVERT: g 120 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7019 (mm) REVERT: g 136 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7685 (tttp) REVERT: h 27 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7431 (pt) REVERT: h 108 THR cc_start: 0.8761 (p) cc_final: 0.8514 (t) REVERT: i 124 PHE cc_start: 0.5499 (m-80) cc_final: 0.5234 (m-80) REVERT: j 16 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5979 (pm20) REVERT: j 67 MET cc_start: 0.7521 (tmm) cc_final: 0.7165 (tmm) REVERT: k 51 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8453 (p) REVERT: k 111 GLN cc_start: 0.8388 (mm110) cc_final: 0.8186 (mm110) REVERT: l 97 ILE cc_start: 0.8800 (mm) cc_final: 0.8575 (mm) REVERT: l 99 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: m 15 MET cc_start: 0.5892 (mmm) cc_final: 0.5425 (mmm) REVERT: m 111 LYS cc_start: 0.7503 (mtmm) cc_final: 0.7035 (mtmm) REVERT: n 26 LYS cc_start: 0.7596 (tttm) cc_final: 0.7243 (ttmt) REVERT: p 10 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8079 (pp) REVERT: p 92 ARG cc_start: 0.6922 (ptt90) cc_final: 0.6460 (ptt-90) REVERT: q 81 MET cc_start: 0.7648 (ptm) cc_final: 0.7326 (ptt) REVERT: q 123 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7367 (ttmt) REVERT: r 59 GLN cc_start: 0.7440 (mt0) cc_final: 0.7206 (mt0) REVERT: s 74 PHE cc_start: 0.8462 (m-80) cc_final: 0.8155 (m-80) REVERT: t 5 LYS cc_start: 0.9042 (tppp) cc_final: 0.8770 (ttpt) REVERT: t 46 LYS cc_start: 0.6846 (mtpp) cc_final: 0.6602 (ttmt) REVERT: t 57 LYS cc_start: 0.7304 (mttp) cc_final: 0.6776 (mttm) REVERT: t 60 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7388 (mttm) REVERT: x 34 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7879 (mm) REVERT: x 56 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8228 (ttpp) REVERT: x 83 LYS cc_start: 0.7300 (tppt) cc_final: 0.7031 (tppt) REVERT: x 91 GLU cc_start: 0.2945 (OUTLIER) cc_final: 0.2506 (mp0) REVERT: x 224 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7022 (mt-10) REVERT: x 308 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7309 (tp30) REVERT: x 343 SER cc_start: 0.8699 (t) cc_final: 0.8360 (p) REVERT: x 356 ASN cc_start: 0.7035 (m110) cc_final: 0.6620 (m-40) REVERT: x 379 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7420 (mtmt) REVERT: x 389 VAL cc_start: 0.4352 (OUTLIER) cc_final: 0.4125 (p) REVERT: x 447 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7438 (mm-30) REVERT: x 467 ASP cc_start: 0.6258 (t0) cc_final: 0.5972 (t0) outliers start: 159 outliers final: 128 residues processed: 1029 average time/residue: 1.3563 time to fit residues: 2403.9939 Evaluate side-chains 1079 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 937 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 145 VAL Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 229 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 100 ARG Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 61 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain q residue 132 GLU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 91 GLU Chi-restraints excluded: chain x residue 141 LEU Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 344 LEU Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 483 ASN Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 7.9990 chunk 1018 optimal weight: 8.9990 chunk 621 optimal weight: 40.0000 chunk 483 optimal weight: 1.9990 chunk 707 optimal weight: 10.0000 chunk 1067 optimal weight: 10.0000 chunk 982 optimal weight: 0.7980 chunk 850 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 656 optimal weight: 8.9990 chunk 521 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN k 87 HIS r 61 GLN ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 164814 Z= 0.300 Angle : 0.619 17.799 246731 Z= 0.309 Chirality : 0.036 0.331 31470 Planarity : 0.005 0.116 13363 Dihedral : 22.936 179.472 82919 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 3.09 % Allowed : 16.77 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.04 (0.10), residues: 6045 helix: -0.87 (0.13), residues: 1751 sheet: -0.88 (0.16), residues: 1038 loop : -1.80 (0.10), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 201 HIS 0.006 0.001 HIS E 56 PHE 0.025 0.002 PHE P 6 TYR 0.019 0.002 TYR Q 47 ARG 0.016 0.001 ARG Q 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12090 Ramachandran restraints generated. 6045 Oldfield, 0 Emsley, 6045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 945 time to evaluate : 5.636 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: 4 22 ARG cc_start: 0.7597 (ptp-110) cc_final: 0.6925 (ptt180) REVERT: 8 181 ASP cc_start: 0.7128 (m-30) cc_final: 0.6478 (p0) REVERT: 8 200 LYS cc_start: 0.8301 (tptm) cc_final: 0.6711 (ptpt) REVERT: 8 210 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6919 (mtmt) REVERT: 8 229 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.6091 (m) REVERT: C 51 THR cc_start: 0.8787 (t) cc_final: 0.8550 (p) REVERT: C 130 ASN cc_start: 0.7931 (t0) cc_final: 0.7703 (t0) REVERT: C 179 SER cc_start: 0.8071 (p) cc_final: 0.7811 (p) REVERT: E 168 ASP cc_start: 0.8201 (t70) cc_final: 0.7865 (t0) REVERT: E 187 ASP cc_start: 0.8045 (p0) cc_final: 0.7815 (p0) REVERT: F 103 MET cc_start: 0.7686 (ttp) cc_final: 0.7327 (ttp) REVERT: F 130 ASP cc_start: 0.7960 (p0) cc_final: 0.7731 (p0) REVERT: G 87 LYS cc_start: 0.7574 (tttt) cc_final: 0.7155 (mmtt) REVERT: G 154 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7528 (ttm-80) REVERT: G 156 ASP cc_start: 0.7732 (t0) cc_final: 0.7358 (t0) REVERT: G 159 LYS cc_start: 0.8525 (mmmm) cc_final: 0.7950 (mmtp) REVERT: H 12 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8245 (tm) REVERT: J 129 GLU cc_start: 0.7640 (tp30) cc_final: 0.7337 (tp30) REVERT: K 92 ASP cc_start: 0.7284 (m-30) cc_final: 0.6982 (m-30) REVERT: O 34 VAL cc_start: 0.8296 (t) cc_final: 0.7739 (m) REVERT: O 60 SER cc_start: 0.8900 (m) cc_final: 0.8584 (t) REVERT: O 98 ASP cc_start: 0.8661 (t0) cc_final: 0.8268 (t0) REVERT: P 29 VAL cc_start: 0.8421 (t) cc_final: 0.8032 (m) REVERT: P 93 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7043 (mtt-85) REVERT: U 2 LYS cc_start: 0.8932 (mttt) cc_final: 0.8504 (mttp) REVERT: Y 31 ASN cc_start: 0.7836 (m110) cc_final: 0.7529 (m-40) REVERT: c 51 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (mp) REVERT: c 87 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7482 (ttp80) REVERT: c 97 GLN cc_start: 0.7153 (pm20) cc_final: 0.6777 (pm20) REVERT: c 170 GLU cc_start: 0.7725 (tp30) cc_final: 0.7329 (tm-30) REVERT: d 45 GLU cc_start: 0.8461 (tp30) cc_final: 0.8034 (tp30) REVERT: d 52 GLU cc_start: 0.6533 (tp30) cc_final: 0.6061 (tp30) REVERT: d 89 LEU cc_start: 0.8534 (mt) cc_final: 0.8081 (mt) REVERT: d 190 LEU cc_start: 0.7879 (pt) cc_final: 0.7329 (pp) REVERT: e 179 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6739 (pt0) REVERT: g 120 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7590 (mt) REVERT: g 136 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: h 27 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7548 (pt) REVERT: h 103 VAL cc_start: 0.8713 (t) cc_final: 0.8289 (m) REVERT: h 108 THR cc_start: 0.8782 (p) cc_final: 0.8547 (t) REVERT: j 16 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.6038 (pm20) REVERT: j 67 MET cc_start: 0.7532 (tmm) cc_final: 0.7189 (tmm) REVERT: k 51 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8480 (p) REVERT: k 111 GLN cc_start: 0.8377 (mm110) cc_final: 0.8158 (mm110) REVERT: l 97 ILE cc_start: 0.8822 (mm) cc_final: 0.8598 (mm) REVERT: m 111 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7082 (mtmm) REVERT: n 26 LYS cc_start: 0.7615 (tttm) cc_final: 0.7265 (ttmt) REVERT: p 10 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8103 (pp) REVERT: q 81 MET cc_start: 0.7674 (ptm) cc_final: 0.7351 (ptt) REVERT: r 59 GLN cc_start: 0.7487 (mt0) cc_final: 0.7210 (mt0) REVERT: s 74 PHE cc_start: 0.8515 (m-80) cc_final: 0.8215 (m-80) REVERT: t 5 LYS cc_start: 0.9030 (tppp) cc_final: 0.8774 (ttpt) REVERT: t 46 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6726 (ttmt) REVERT: t 57 LYS cc_start: 0.7312 (mttp) cc_final: 0.6718 (mmmt) REVERT: t 60 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7580 (mttm) REVERT: x 34 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7903 (mm) REVERT: x 56 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8366 (ttpp) REVERT: x 83 LYS cc_start: 0.7320 (tppt) cc_final: 0.7046 (tppt) REVERT: x 91 GLU cc_start: 0.3090 (OUTLIER) cc_final: 0.2621 (mp0) REVERT: x 224 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7090 (mt-10) REVERT: x 233 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.7053 (mtp-110) REVERT: x 308 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7275 (tp30) REVERT: x 343 SER cc_start: 0.8755 (t) cc_final: 0.8345 (p) REVERT: x 356 ASN cc_start: 0.7197 (m110) cc_final: 0.6784 (m110) REVERT: x 364 PHE cc_start: 0.7747 (m-10) cc_final: 0.7455 (m-10) REVERT: x 379 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7618 (mtmt) REVERT: x 389 VAL cc_start: 0.4403 (OUTLIER) cc_final: 0.4183 (p) REVERT: x 447 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7421 (mm-30) REVERT: x 467 ASP cc_start: 0.6297 (t0) cc_final: 0.6003 (t0) outliers start: 155 outliers final: 138 residues processed: 1024 average time/residue: 1.3779 time to fit residues: 2440.4701 Evaluate side-chains 1084 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 932 time to evaluate : 6.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 100 LEU Chi-restraints excluded: chain 8 residue 145 VAL Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain 8 residue 209 LEU Chi-restraints excluded: chain 8 residue 229 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 25 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 100 ARG Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 61 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain d residue 83 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 102 PHE Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 179 GLN Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain e residue 192 ILE Chi-restraints excluded: chain e residue 193 GLU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 104 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 27 SER Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 85 VAL Chi-restraints excluded: chain x residue 91 GLU Chi-restraints excluded: chain x residue 141 LEU Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 183 LEU Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 210 LEU Chi-restraints excluded: chain x residue 212 VAL Chi-restraints excluded: chain x residue 267 THR Chi-restraints excluded: chain x residue 273 VAL Chi-restraints excluded: chain x residue 344 LEU Chi-restraints excluded: chain x residue 377 SER Chi-restraints excluded: chain x residue 389 VAL Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 455 LEU Chi-restraints excluded: chain x residue 456 THR Chi-restraints excluded: chain x residue 483 ASN Chi-restraints excluded: chain x residue 495 ILE Chi-restraints excluded: chain x residue 506 CYS Chi-restraints excluded: chain x residue 529 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 20.0000 chunk 905 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 784 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 236 optimal weight: 5.9990 chunk 851 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 874 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 ASN ** p 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090967 restraints weight = 225223.546| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.14 r_work: 0.2866 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 164814 Z= 0.401 Angle : 0.703 18.223 246731 Z= 0.348 Chirality : 0.041 0.345 31470 Planarity : 0.006 0.118 13363 Dihedral : 23.001 178.969 82919 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 3.27 % Allowed : 16.97 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.19 (0.10), residues: 6045 helix: -1.06 (0.12), residues: 1777 sheet: -0.89 (0.17), residues: 991 loop : -1.87 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 22 HIS 0.008 0.002 HIS L 126 PHE 0.028 0.002 PHE P 6 TYR 0.025 0.002 TYR Q 47 ARG 0.020 0.001 ARG Q 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38938.69 seconds wall clock time: 680 minutes 23.07 seconds (40823.07 seconds total)