Starting phenix.real_space_refine on Sun Apr 14 15:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7y_15905/04_2024/8b7y_15905_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4614 5.49 5 Mg 237 5.21 5 S 135 5.16 5 C 70285 2.51 5 N 26274 2.21 5 O 39462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141008 Number of models: 1 Model: "" Number of chains: 70 Chain: "I" Number of atoms: 62225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 62225 Classifications: {'RNA': 2898} Modifications used: {'rna2p': 4, 'rna2p_pur': 281, 'rna2p_pyr': 149, 'rna3p': 14, 'rna3p_pur': 1386, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 434, 'rna3p': 2463} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 58, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "O" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "R" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "V" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "e" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "g" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "h" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "n" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "C" Number of atoms: 32599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32599 Classifications: {'RNA': 1519} Modifications used: {'rna2p_pur': 127, 'rna2p_pyr': 84, 'rna3p_pur': 741, 'rna3p_pyr': 567} Link IDs: {'rna2p': 211, 'rna3p': 1307} Chain breaks: 2 Chain: "D" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "G" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "H" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "P" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "r" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "v" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "y" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "5" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "6" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "z" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 118 Unusual residues: {'AG2': 1, 'ALQ': 1, 'IB9': 1} Classifications: {'peptide': 13, 'undetermined': 3} Modifications used: {'PEPT-D': 6} Link IDs: {'TRANS': 11, None: 4} Not linked: pdbres="ALQ z 1 " pdbres="RXL z 2 " Not linked: pdbres="DVA z 6 " pdbres="IB9 z 7 " Not linked: pdbres="IB9 z 7 " pdbres="DVA z 8 " Not linked: pdbres="DHV z 15 " pdbres="AG2 z 16 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'RXL:plan-1': 2, 'MAA:plan-1': 1, 'RX9:plan-1': 1, 'ALQ:plan-1': 1, 'IB9:plan-2': 1, 'DHV:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Unusual residues: {' MG': 136} Classifications: {'undetermined': 136} Link IDs: {None: 135} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 107 Unusual residues: {' MG': 87, 'SPD': 2} Classifications: {'undetermined': 89} Link IDs: {None: 88} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "z" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 87092 SG CYS m 11 116.451 147.001 180.352 1.00 9.56 S ATOM 87117 SG CYS m 14 114.795 150.460 178.336 1.00 8.51 S ATOM 87220 SG CYS m 27 118.178 150.043 179.988 1.00 10.03 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG I3124 " occ=0.50 residue: pdb="MG MG I3125 " occ=0.50 Time building chain proxies: 54.98, per 1000 atoms: 0.39 Number of scatterers: 141008 At special positions: 0 Unit cell: (264.303, 275.886, 227.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 135 16.00 P 4614 15.00 Mg 237 11.99 O 39462 8.00 N 26274 7.00 C 70285 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 63.00 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " Number of angles added : 3 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA z 5 " pdb=" CB DVA z 6 " pdb=" CB DVA z 8 " pdb=" CB DAR z 10 " pdb=" CB DVA z 12 " pdb=" CB DAL z 14 " Input volumes are d-peptide like pdb=" CB DHV z 15 " Number of C-beta restraints generated: 9760 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: 162 helices and 69 sheets defined 38.9% alpha, 20.1% beta 1425 base pairs and 2528 stacking pairs defined. Time for finding SS restraints: 74.65 Creating SS restraints... Processing helix chain 'K' and resid 12 through 17 removed outlier: 5.119A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 17' Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.829A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.877A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 268 removed outlier: 6.497A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'L' and resid 56 through 61 removed outlier: 5.550A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 72 Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.499A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 39 through 44 Processing helix chain 'M' and resid 24 through 41 removed outlier: 5.595A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 165 removed outlier: 4.814A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 5.511A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'O' and resid 2 through 7 removed outlier: 3.778A pdb=" N LYS O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 2 through 7' Processing helix chain 'O' and resid 60 through 81 removed outlier: 3.510A pdb=" N THR O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 3.515A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.194A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 4.004A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 removed outlier: 4.418A pdb=" N LYS R 72 " --> pdb=" O ASN R 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 67 through 72' Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.619A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER S 109 " --> pdb=" O ARG S 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 104 through 109' Processing helix chain 'S' and resid 110 through 119 removed outlier: 5.048A pdb=" N LYS S 114 " --> pdb=" O GLU S 110 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE S 115 " --> pdb=" O LYS S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 5.512A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 68 through 75 removed outlier: 7.104A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 83 removed outlier: 4.441A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 99 Processing helix chain 'T' and resid 128 through 139 Processing helix chain 'U' and resid 42 through 58 Processing helix chain 'U' and resid 109 through 125 removed outlier: 4.256A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) Proline residue: U 125 - end of helix Processing helix chain 'V' and resid 13 through 32 Processing helix chain 'V' and resid 37 through 58 removed outlier: 4.230A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 4.253A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP V 58 " --> pdb=" O LEU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 3.842A pdb=" N LEU V 83 " --> pdb=" O LEU V 79 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY V 84 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Proline residue: V 85 - end of helix Processing helix chain 'W' and resid 2 through 22 removed outlier: 4.215A pdb=" N ALA W 6 " --> pdb=" O ASP W 2 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 63 removed outlier: 4.118A pdb=" N GLN W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'X' and resid 2 through 13 removed outlier: 3.647A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.840A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG X 103 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR X 104 " --> pdb=" O LEU X 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 97 through 104' Processing helix chain 'Y' and resid 6 through 22 removed outlier: 3.743A pdb=" N LYS Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 32 through 37 Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.777A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 91 through 101 Processing helix chain 'Y' and resid 102 through 118 Processing helix chain 'a' and resid 13 through 25 removed outlier: 4.325A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.806A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 70 removed outlier: 4.420A pdb=" N LEU a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS a 70 " --> pdb=" O ILE a 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 65 through 70' Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.566A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 27 removed outlier: 4.797A pdb=" N SER b 21 " --> pdb=" O SER b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'c' and resid 66 through 71 removed outlier: 4.030A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA c 71 " --> pdb=" O VAL c 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 66 through 71' Processing helix chain 'd' and resid 13 through 24 removed outlier: 3.758A pdb=" N ASN d 24 " --> pdb=" O LEU d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 3.900A pdb=" N SER d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 63 Processing helix chain 'f' and resid 64 through 75 removed outlier: 3.507A pdb=" N GLU f 70 " --> pdb=" O THR f 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 10 removed outlier: 5.825A pdb=" N LEU g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 Processing helix chain 'g' and resid 39 through 62 removed outlier: 4.397A pdb=" N LEU g 43 " --> pdb=" O GLN g 39 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL g 46 " --> pdb=" O LEU g 42 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP g 49 " --> pdb=" O GLN g 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 28 Processing helix chain 'h' and resid 41 through 52 Processing helix chain 'i' and resid 9 through 19 removed outlier: 4.795A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 31 Proline residue: j 31 - end of helix No H-bonds generated for 'chain 'j' and resid 26 through 31' Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 17 through 24 removed outlier: 4.344A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 38 Processing helix chain 'l' and resid 7 through 14 removed outlier: 3.522A pdb=" N ARG l 13 " --> pdb=" O GLY l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.248A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 32 through 37' Processing helix chain 'l' and resid 38 through 46 Proline residue: l 46 - end of helix Processing helix chain 'l' and resid 51 through 63 removed outlier: 4.830A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Proline residue: l 63 - end of helix Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 27 through 32 removed outlier: 5.523A pdb=" N PHE D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 64 Proline residue: D 48 - end of helix removed outlier: 3.667A pdb=" N LYS D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.968A pdb=" N SER D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.646A pdb=" N LEU D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 130' Processing helix chain 'D' and resid 131 through 148 removed outlier: 4.055A pdb=" N LEU D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 206 through 227 removed outlier: 3.577A pdb=" N LEU D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 28 through 48 removed outlier: 3.761A pdb=" N ASN E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 108 through 113 removed outlier: 4.174A pdb=" N ASP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 113' Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 129 through 145 Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.176A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 68 through 83 removed outlier: 5.243A pdb=" N LYS F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 98 through 106 removed outlier: 4.446A pdb=" N MET F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 121 removed outlier: 7.034A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 166 removed outlier: 3.995A pdb=" N ALA F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.887A pdb=" N SER F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.925A pdb=" N ILE F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 71 removed outlier: 3.594A pdb=" N ARG G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 132 through 147 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 160 through 165 removed outlier: 3.602A pdb=" N LEU G 165 " --> pdb=" O VAL G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 33 removed outlier: 3.545A pdb=" N VAL H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) Proline residue: H 19 - end of helix Processing helix chain 'H' and resid 67 through 81 removed outlier: 3.541A pdb=" N ILE H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 31 Processing helix chain 'N' and resid 35 through 55 Processing helix chain 'N' and resid 57 through 70 removed outlier: 4.826A pdb=" N GLU N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 111 removed outlier: 3.780A pdb=" N ASN N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 130 Processing helix chain 'N' and resid 132 through 149 Processing helix chain 'P' and resid 5 through 21 Processing helix chain 'P' and resid 30 through 44 Processing helix chain 'P' and resid 112 through 120 Processing helix chain 'Q' and resid 34 through 39 Processing helix chain 'Q' and resid 41 through 56 removed outlier: 3.651A pdb=" N ARG Q 45 " --> pdb=" O ARG Q 41 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 71 through 92 Processing helix chain 'Q' and resid 93 through 102 removed outlier: 4.249A pdb=" N GLU Q 97 " --> pdb=" O SER Q 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.721A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY o 33 " --> pdb=" O ALA o 29 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.869A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.965A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 60 through 75 Processing helix chain 'p' and resid 92 through 104 removed outlier: 4.525A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.106A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY q 118 " --> pdb=" O ARG q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 113 through 118' Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.122A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 44 through 49 removed outlier: 5.224A pdb=" N SER r 49 " --> pdb=" O ILE r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 63 removed outlier: 3.910A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.514A pdb=" N LYS s 19 " --> pdb=" O ALA s 15 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.687A pdb=" N SER s 32 " --> pdb=" O LYS s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.633A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 43 removed outlier: 4.545A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 80 Processing helix chain 'w' and resid 11 through 17 removed outlier: 3.664A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.598A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.223A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 37 removed outlier: 3.593A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 Processing helix chain '5' and resid 11 through 27 Processing helix chain '5' and resid 28 through 37 removed outlier: 4.480A pdb=" N PHE 5 37 " --> pdb=" O ARG 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 68 removed outlier: 3.524A pdb=" N LYS 5 59 " --> pdb=" O ARG 5 55 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG 5 67 " --> pdb=" O GLU 5 63 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'K' and resid 33 through 37 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.660A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE K 91 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.630A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 90 through 96 removed outlier: 5.378A pdb=" N ASN K 90 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L' and resid 3 through 8 removed outlier: 4.389A pdb=" N SER L 199 " --> pdb=" O LYS L 8 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L' and resid 11 through 16 removed outlier: 3.613A pdb=" N ILE L 22 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 189 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP L 181 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG L 179 " --> pdb=" O LEU L 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.816A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN L 94 " --> pdb=" O VAL L 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L' and resid 105 through 108 removed outlier: 5.993A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.671A pdb=" N LEU M 5 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'M' and resid 42 through 47 removed outlier: 7.410A pdb=" N GLY M 42 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP M 91 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 12, first strand: chain 'O' and resid 23 through 27 Processing sheet with id= 13, first strand: chain 'O' and resid 41 through 45 removed outlier: 3.532A pdb=" N GLU O 42 " --> pdb=" O GLY O 53 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 82 through 89 removed outlier: 5.014A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL O 132 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS O 134 " --> pdb=" O THR O 122 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 94 through 98 removed outlier: 3.747A pdb=" N SER O 106 " --> pdb=" O ARG O 95 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'R' and resid 52 through 57 removed outlier: 5.185A pdb=" N ASP R 19 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'R' and resid 74 through 78 removed outlier: 6.969A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'S' and resid 18 through 21 removed outlier: 4.173A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU S 86 " --> pdb=" O ALA S 11 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS S 59 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP S 37 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.914A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'U' and resid 71 through 74 Processing sheet with id= 21, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.647A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'V' and resid 33 through 36 removed outlier: 6.853A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 49 through 52 removed outlier: 3.708A pdb=" N VAL W 28 " --> pdb=" O ASP W 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.242A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'X' and resid 49 through 52 removed outlier: 3.511A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER X 57 " --> pdb=" O THR X 76 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Z' and resid 11 through 15 removed outlier: 3.619A pdb=" N MET Z 40 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 18 through 23 removed outlier: 4.566A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU Z 31 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 57 through 60 Processing sheet with id= 29, first strand: chain 'Z' and resid 65 through 68 removed outlier: 3.747A pdb=" N ALA Z 65 " --> pdb=" O ASP Z 95 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Z' and resid 71 through 78 removed outlier: 4.059A pdb=" N TYR Z 83 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'a' and resid 2 through 8 removed outlier: 4.593A pdb=" N THR a 100 " --> pdb=" O GLY a 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS a 73 " --> pdb=" O VAL a 106 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'a' and resid 81 through 88 removed outlier: 4.168A pdb=" N ARG a 92 " --> pdb=" O ARG a 88 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 12 through 15 removed outlier: 5.523A pdb=" N VAL b 31 " --> pdb=" O HIS b 15 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG b 73 " --> pdb=" O HIS b 70 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 40 through 45 removed outlier: 4.714A pdb=" N ASN c 40 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS c 61 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS c 44 " --> pdb=" O VAL c 59 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'c' and resid 82 through 86 removed outlier: 5.579A pdb=" N ARG c 82 " --> pdb=" O LYS c 97 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG c 94 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU c 101 " --> pdb=" O PHE c 96 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 75 through 79 removed outlier: 3.791A pdb=" N ILE d 89 " --> pdb=" O PRO d 27 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE d 2 " --> pdb=" O VAL d 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA d 6 " --> pdb=" O VAL d 64 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 71 through 74 removed outlier: 6.141A pdb=" N LYS d 71 " --> pdb=" O ALA d 94 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 51 through 54 removed outlier: 4.201A pdb=" N THR e 58 " --> pdb=" O GLY e 54 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 65 through 71 Processing sheet with id= 40, first strand: chain 'f' and resid 12 through 19 removed outlier: 3.909A pdb=" N THR f 25 " --> pdb=" O ASN f 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER f 19 " --> pdb=" O ASN f 23 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'f' and resid 35 through 41 Processing sheet with id= 42, first strand: chain 'h' and resid 34 through 39 removed outlier: 4.410A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS h 6 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'i' and resid 28 through 31 removed outlier: 6.776A pdb=" N SER i 29 " --> pdb=" O LYS i 37 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS i 37 " --> pdb=" O SER i 29 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP i 31 " --> pdb=" O GLY i 35 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'j' and resid 19 through 24 removed outlier: 5.796A pdb=" N HIS j 19 " --> pdb=" O SER j 13 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS j 10 " --> pdb=" O ALA j 52 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA j 52 " --> pdb=" O LYS j 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE j 48 " --> pdb=" O SER j 14 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU j 51 " --> pdb=" O LEU j 34 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU j 34 " --> pdb=" O GLU j 51 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.635A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 1 through 5 removed outlier: 5.943A pdb=" N HIS m 33 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N CYS m 27 " --> pdb=" O HIS m 33 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE m 23 " --> pdb=" O GLN m 37 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 15 through 18 removed outlier: 4.937A pdb=" N HIS D 15 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N HIS D 39 " --> pdb=" O GLY D 17 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 89 through 93 removed outlier: 3.620A pdb=" N ALA D 185 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'E' and resid 54 through 59 removed outlier: 3.551A pdb=" N ARG E 54 " --> pdb=" O HIS E 69 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 64 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 100 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 66 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.628A pdb=" N GLY E 155 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'F' and resid 141 through 144 removed outlier: 3.730A pdb=" N ASP F 141 " --> pdb=" O PHE F 182 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'G' and resid 11 through 16 removed outlier: 6.792A pdb=" N LEU G 36 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'G' and resid 83 through 88 removed outlier: 7.337A pdb=" N HIS G 83 " --> pdb=" O PRO G 98 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG G 93 " --> pdb=" O TYR G 128 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA G 99 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN G 122 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 32 through 41 removed outlier: 7.081A pdb=" N ARG G 45 " --> pdb=" O ASP G 41 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'H' and resid 38 through 42 removed outlier: 5.006A pdb=" N TYR H 59 " --> pdb=" O TRP H 42 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS H 3 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET H 90 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET H 88 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG H 86 " --> pdb=" O MET H 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.842A pdb=" N GLY H 43 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS H 55 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'N' and resid 72 through 79 removed outlier: 6.685A pdb=" N THR N 72 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL N 91 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG N 78 " --> pdb=" O TYR N 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 23 through 29 removed outlier: 5.589A pdb=" N ALA P 23 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP P 48 " --> pdb=" O THR P 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 74 through 77 removed outlier: 4.327A pdb=" N SER P 74 " --> pdb=" O ALA P 130 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL P 103 " --> pdb=" O ILE P 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 5 through 11 removed outlier: 4.138A pdb=" N ARG Q 18 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR Q 66 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE Q 20 " --> pdb=" O TYR Q 64 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR Q 64 " --> pdb=" O PHE Q 20 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Q 22 " --> pdb=" O ASP Q 62 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU Q 61 " --> pdb=" O ASN Q 25 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS Q 27 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.126A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 44 through 52 removed outlier: 3.685A pdb=" N GLU o 47 " --> pdb=" O ILE o 67 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 42 through 45 removed outlier: 3.615A pdb=" N GLY p 43 " --> pdb=" O ILE p 34 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA p 21 " --> pdb=" O GLU p 83 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL p 84 " --> pdb=" O THR p 108 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.032A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 36 through 41 removed outlier: 3.738A pdb=" N ARG q 36 " --> pdb=" O ARG q 54 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.560A pdb=" N HIS u 9 " --> pdb=" O PHE u 16 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.838A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'x' and resid 31 through 34 removed outlier: 4.064A pdb=" N LEU x 31 " --> pdb=" O THR x 48 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA x 50 " --> pdb=" O LEU x 31 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 1795 hydrogen bonds defined for protein. 5325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3527 hydrogen bonds 5482 hydrogen bond angles 0 basepair planarities 1425 basepair parallelities 2528 stacking parallelities Total time for adding SS restraints: 259.83 Time building geometry restraints manager: 67.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11126 1.28 - 1.42: 56738 1.42 - 1.55: 75849 1.55 - 1.69: 9224 1.69 - 1.82: 243 Bond restraints: 153180 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.22e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N3 5MU I1939 " pdb=" C4 5MU I1939 " ideal model delta sigma weight residual 1.182 1.378 -0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 153175 not shown) Histogram of bond angle deviations from ideal: 99.04 - 107.23: 31575 107.23 - 115.43: 99477 115.43 - 123.62: 76208 123.62 - 131.82: 21295 131.82 - 140.01: 1107 Bond angle restraints: 229662 Sorted by residual: angle pdb=" CG1 RXL z 2 " pdb=" CB RXL z 2 " pdb=" CG2 RXL z 2 " ideal model delta sigma weight residual 68.18 114.21 -46.03 3.00e+00 1.11e-01 2.35e+02 angle pdb=" CG1 RXL z 9 " pdb=" CB RXL z 9 " pdb=" CG2 RXL z 9 " ideal model delta sigma weight residual 68.18 114.07 -45.89 3.00e+00 1.11e-01 2.34e+02 angle pdb=" CA RXL z 9 " pdb=" CB RXL z 9 " pdb=" CG1 RXL z 9 " ideal model delta sigma weight residual 85.85 123.96 -38.11 3.00e+00 1.11e-01 1.61e+02 angle pdb=" CA RXL z 2 " pdb=" CB RXL z 2 " pdb=" CG1 RXL z 2 " ideal model delta sigma weight residual 85.85 122.67 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CA RXL z 9 " pdb=" CB RXL z 9 " pdb=" CG2 RXL z 9 " ideal model delta sigma weight residual 152.68 121.98 30.70 3.00e+00 1.11e-01 1.05e+02 ... (remaining 229657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 85356 35.95 - 71.91: 11441 71.91 - 107.86: 1325 107.86 - 143.82: 28 143.82 - 179.77: 18 Dihedral angle restraints: 98168 sinusoidal: 83034 harmonic: 15134 Sorted by residual: dihedral pdb=" N IB9 z 7 " pdb=" C IB9 z 7 " pdb=" CA IB9 z 7 " pdb=" CB IB9 z 7 " ideal model delta harmonic sigma weight residual 122.80 33.50 89.30 0 2.50e+00 1.60e-01 1.28e+03 dihedral pdb=" C RXL z 9 " pdb=" N RXL z 9 " pdb=" CA RXL z 9 " pdb=" CB RXL z 9 " ideal model delta harmonic sigma weight residual -122.60 -179.89 57.29 0 2.50e+00 1.60e-01 5.25e+02 dihedral pdb=" N RXL z 9 " pdb=" C RXL z 9 " pdb=" CA RXL z 9 " pdb=" CB RXL z 9 " ideal model delta harmonic sigma weight residual 122.80 179.88 -57.08 0 2.50e+00 1.60e-01 5.21e+02 ... (remaining 98165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.035: 29357 1.035 - 2.070: 0 2.070 - 3.105: 0 3.105 - 4.141: 0 4.141 - 5.176: 1 Chirality restraints: 29358 Sorted by residual: chirality pdb=" CB DVA z 8 " pdb=" CA DVA z 8 " pdb=" CG1 DVA z 8 " pdb=" CG2 DVA z 8 " both_signs ideal model delta sigma weight residual False -2.63 2.55 -5.18 2.00e-01 2.50e+01 6.70e+02 chirality pdb=" P G n 2 " pdb=" OP1 G n 2 " pdb=" OP2 G n 2 " pdb=" O5' G n 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" P C n 17 " pdb=" OP1 C n 17 " pdb=" OP2 C n 17 " pdb=" O5' C n 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 29355 not shown) Planarity restraints: 11932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.063 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' OMC I2498 " 0.436 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.593 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.658 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.162 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 1.000 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.229 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.903 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.002 2.00e-02 2.50e+03 5.82e-01 7.63e+03 pdb=" C4' OMG I2251 " 0.449 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.737 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.541 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.235 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.867 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.215 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.044 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' 2MG I2445 " -0.424 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.633 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.608 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.585 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.937 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.871 2.00e-02 2.50e+03 ... (remaining 11929 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 153 2.41 - 3.03: 79027 3.03 - 3.66: 273324 3.66 - 4.28: 440902 4.28 - 4.90: 575744 Nonbonded interactions: 1369150 Sorted by model distance: nonbonded pdb=" OP2 U I1636 " pdb="MG MG I3072 " model vdw 1.792 2.170 nonbonded pdb=" OP2 A C1110 " pdb="MG MG C1602 " model vdw 1.819 2.170 nonbonded pdb=" OP2 C I2575 " pdb="MG MG I3084 " model vdw 1.828 2.170 nonbonded pdb=" OP2 A I1265 " pdb="MG MG I3089 " model vdw 1.833 2.170 nonbonded pdb=" OP2 C I2611 " pdb="MG MG I3134 " model vdw 1.866 2.170 ... (remaining 1369145 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=0.50 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 15.530 Check model and map are aligned: 1.590 Set scattering table: 1.020 Process input model: 580.270 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 617.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.005 0.359 153180 Z= 0.319 Angle : 0.759 46.032 229662 Z= 0.438 Chirality : 0.055 5.176 29358 Planarity : 0.014 0.599 11932 Dihedral : 23.882 179.769 88408 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.70 % Favored : 93.54 % Rotamer: Outliers : 3.80 % Allowed : 6.63 % Favored : 89.56 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 5214 helix: 0.58 (0.11), residues: 1782 sheet: -2.27 (0.15), residues: 983 loop : -1.51 (0.11), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP x 34 HIS 0.009 0.002 HIS K 230 PHE 0.037 0.003 PHE D 90 TYR 0.031 0.003 TYR F 103 ARG 0.013 0.001 ARG Q 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1318 time to evaluate : 6.006 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: K 35 GLU cc_start: 0.6804 (tt0) cc_final: 0.6506 (tt0) REVERT: K 114 ASP cc_start: 0.6362 (m-30) cc_final: 0.6130 (m-30) REVERT: K 146 MET cc_start: 0.7830 (mtp) cc_final: 0.7560 (mtp) REVERT: K 272 SER cc_start: 0.5376 (m) cc_final: 0.5062 (p) REVERT: L 30 GLU cc_start: 0.5880 (mt-10) cc_final: 0.5439 (mt-10) REVERT: L 177 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8305 (t) REVERT: M 21 ARG cc_start: 0.7234 (ptp-170) cc_final: 0.6730 (ptm160) REVERT: M 72 SER cc_start: 0.8669 (t) cc_final: 0.8258 (p) REVERT: M 115 GLN cc_start: 0.6678 (mt0) cc_final: 0.6353 (mt0) REVERT: M 136 GLN cc_start: 0.7558 (tp40) cc_final: 0.7221 (mm-40) REVERT: O 102 VAL cc_start: 0.7038 (t) cc_final: 0.6715 (t) REVERT: R 13 ARG cc_start: 0.6915 (mtt90) cc_final: 0.6407 (mmt90) REVERT: R 49 ASP cc_start: 0.7269 (t0) cc_final: 0.7044 (t0) REVERT: S 7 MET cc_start: 0.8337 (mmm) cc_final: 0.7902 (mmm) REVERT: S 53 LYS cc_start: 0.7004 (mmtm) cc_final: 0.6659 (mmtt) REVERT: S 104 THR cc_start: 0.7542 (p) cc_final: 0.6994 (p) REVERT: S 121 GLU cc_start: 0.6559 (tt0) cc_final: 0.6231 (tm-30) REVERT: T 1 MET cc_start: 0.7152 (ttp) cc_final: 0.6933 (ttp) REVERT: T 5 THR cc_start: 0.7080 (m) cc_final: 0.6863 (t) REVERT: U 12 MET cc_start: 0.7748 (ttp) cc_final: 0.7459 (ttm) REVERT: U 134 THR cc_start: 0.5887 (p) cc_final: 0.5666 (t) REVERT: V 18 GLN cc_start: 0.7831 (tt0) cc_final: 0.7589 (tt0) REVERT: W 80 GLU cc_start: 0.5809 (mt-10) cc_final: 0.5521 (mt-10) REVERT: X 2 SER cc_start: 0.6134 (p) cc_final: 0.5932 (p) REVERT: X 104 THR cc_start: 0.7345 (p) cc_final: 0.7038 (t) REVERT: Y 49 ASP cc_start: 0.7711 (m-30) cc_final: 0.7476 (m-30) REVERT: Z 13 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7494 (ttp80) REVERT: a 22 ASP cc_start: 0.7001 (m-30) cc_final: 0.6699 (m-30) REVERT: b 76 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.7343 (ttt-90) REVERT: b 93 LEU cc_start: 0.2995 (OUTLIER) cc_final: 0.2540 (mp) REVERT: c 33 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: d 51 GLN cc_start: 0.7520 (pp30) cc_final: 0.7214 (pp30) REVERT: e 78 LYS cc_start: 0.7501 (mppt) cc_final: 0.7244 (mmtm) REVERT: g 2 LYS cc_start: 0.3557 (OUTLIER) cc_final: 0.2625 (mtmt) REVERT: g 53 VAL cc_start: 0.8599 (t) cc_final: 0.8328 (t) REVERT: i 15 MET cc_start: 0.8164 (mtt) cc_final: 0.7877 (mtp) REVERT: i 53 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7857 (tptm) REVERT: j 32 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6219 (pp20) REVERT: k 25 LYS cc_start: 0.6887 (ttpp) cc_final: 0.6674 (tptp) REVERT: l 16 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7815 (tmtm) REVERT: l 49 MET cc_start: 0.7715 (mmm) cc_final: 0.7505 (mmm) REVERT: D 9 MET cc_start: 0.5085 (mmt) cc_final: 0.3926 (ptp) REVERT: D 113 ARG cc_start: 0.5911 (tpt170) cc_final: 0.5663 (tpt90) REVERT: D 129 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2893 (mt) REVERT: D 213 TYR cc_start: 0.6795 (m-80) cc_final: 0.6515 (m-80) REVERT: E 8 ASN cc_start: 0.7614 (t0) cc_final: 0.7387 (t0) REVERT: E 21 THR cc_start: 0.6864 (p) cc_final: 0.6615 (p) REVERT: E 129 MET cc_start: 0.6347 (mmm) cc_final: 0.6136 (tpp) REVERT: E 135 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6998 (mmpt) REVERT: F 33 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6108 (ptpt) REVERT: F 85 ASN cc_start: 0.6409 (t0) cc_final: 0.6122 (m-40) REVERT: F 89 ASN cc_start: 0.7140 (m-40) cc_final: 0.6727 (m110) REVERT: F 104 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.6103 (tpm170) REVERT: G 13 GLU cc_start: 0.5783 (mt-10) cc_final: 0.5454 (mp0) REVERT: G 64 MET cc_start: 0.7492 (mmt) cc_final: 0.7047 (mmt) REVERT: G 77 ASN cc_start: 0.6721 (t0) cc_final: 0.6213 (t0) REVERT: G 103 THR cc_start: 0.7825 (m) cc_final: 0.7511 (m) REVERT: H 45 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7334 (mtm110) REVERT: H 100 SER cc_start: 0.6977 (p) cc_final: 0.6646 (t) REVERT: P 5 ASP cc_start: 0.6841 (t0) cc_final: 0.6629 (t0) REVERT: P 73 GLU cc_start: 0.6514 (tt0) cc_final: 0.6145 (tt0) REVERT: Q 85 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.4931 (mpp80) REVERT: o 27 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5551 (mm-30) REVERT: o 60 ASP cc_start: 0.6893 (m-30) cc_final: 0.6629 (m-30) REVERT: p 59 THR cc_start: 0.7758 (p) cc_final: 0.7318 (p) REVERT: p 109 ASN cc_start: 0.5746 (p0) cc_final: 0.5424 (p0) REVERT: r 19 LEU cc_start: 0.7178 (mt) cc_final: 0.6946 (mt) REVERT: r 30 SER cc_start: 0.7607 (t) cc_final: 0.7309 (t) REVERT: r 83 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6718 (tp) REVERT: s 21 PHE cc_start: 0.6150 (t80) cc_final: 0.5940 (t80) REVERT: s 46 LEU cc_start: 0.7245 (mt) cc_final: 0.7012 (mp) REVERT: t 8 THR cc_start: 0.8300 (m) cc_final: 0.8076 (p) REVERT: u 17 TYR cc_start: 0.7955 (m-80) cc_final: 0.7754 (m-80) REVERT: u 25 ARG cc_start: 0.7420 (mtm180) cc_final: 0.7182 (mpp80) REVERT: u 33 ILE cc_start: 0.8066 (mt) cc_final: 0.7813 (mt) REVERT: u 45 GLU cc_start: 0.4742 (OUTLIER) cc_final: 0.3936 (mp0) REVERT: u 50 THR cc_start: 0.6096 (m) cc_final: 0.5765 (t) REVERT: v 14 SER cc_start: 0.7027 (t) cc_final: 0.6619 (m) REVERT: v 20 SER cc_start: 0.6056 (m) cc_final: 0.5834 (t) REVERT: w 35 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4826 (tp30) REVERT: x 6 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6969 (ttpm) REVERT: x 67 VAL cc_start: 0.7100 (t) cc_final: 0.6836 (m) REVERT: x 73 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6069 (mt-10) REVERT: y 18 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6745 (ttp80) REVERT: y 48 GLN cc_start: 0.6190 (tp-100) cc_final: 0.5976 (tp-100) REVERT: 5 60 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.3908 (tm) REVERT: 5 63 GLU cc_start: 0.3628 (OUTLIER) cc_final: 0.2820 (mm-30) outliers start: 165 outliers final: 26 residues processed: 1417 average time/residue: 2.1869 time to fit residues: 4352.1101 Evaluate side-chains 896 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 852 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 53 LYS Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 32 GLU Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain x residue 6 LYS Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 818 optimal weight: 9.9990 chunk 734 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 495 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 chunk 759 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 461 optimal weight: 8.9990 chunk 565 optimal weight: 10.0000 chunk 879 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 86 ASN K 153 GLN M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 GLN S 90 ASN Y 37 GLN Z 86 GLN a 61 ASN b 48 GLN g 31 GLN g 39 GLN i 5 GLN j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN N 122 ASN ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 GLN Q 110 GLN Q 126 GLN p 40 ASN p 81 ASN q 112 GLN r 52 GLN t 37 ASN t 80 GLN u 29 ASN v 9 GLN y 52 ASN y 55 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 153180 Z= 0.475 Angle : 0.884 33.251 229662 Z= 0.441 Chirality : 0.049 0.396 29358 Planarity : 0.008 0.146 11932 Dihedral : 24.137 179.692 78017 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.93 % Favored : 94.74 % Rotamer: Outliers : 7.39 % Allowed : 16.79 % Favored : 75.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.57 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5214 helix: 0.36 (0.12), residues: 1802 sheet: -1.83 (0.15), residues: 963 loop : -1.46 (0.11), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP U 64 HIS 0.010 0.002 HIS K 232 PHE 0.028 0.003 PHE x 10 TYR 0.022 0.003 TYR Q 90 ARG 0.010 0.001 ARG l 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 830 time to evaluate : 6.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 146 MET cc_start: 0.7817 (mtp) cc_final: 0.7525 (mtp) REVERT: L 177 VAL cc_start: 0.8532 (p) cc_final: 0.8257 (t) REVERT: M 6 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.6170 (mtpt) REVERT: M 21 ARG cc_start: 0.6964 (ptp-170) cc_final: 0.6478 (ptm160) REVERT: M 136 GLN cc_start: 0.7668 (tp40) cc_final: 0.7313 (mm-40) REVERT: O 6 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6010 (ttpp) REVERT: O 10 VAL cc_start: 0.5742 (OUTLIER) cc_final: 0.5423 (t) REVERT: S 7 MET cc_start: 0.8286 (mmm) cc_final: 0.7754 (mmm) REVERT: S 53 LYS cc_start: 0.6944 (mmtm) cc_final: 0.6544 (mmtt) REVERT: S 114 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7095 (ttmt) REVERT: T 1 MET cc_start: 0.7355 (ttp) cc_final: 0.7050 (ttp) REVERT: T 5 THR cc_start: 0.7111 (m) cc_final: 0.6889 (t) REVERT: T 13 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7633 (mptm) REVERT: T 123 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6565 (ttp80) REVERT: U 40 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6167 (mtm180) REVERT: U 134 THR cc_start: 0.5932 (p) cc_final: 0.5158 (m) REVERT: W 69 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: W 76 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7382 (tptm) REVERT: X 3 ASN cc_start: 0.6545 (m-40) cc_final: 0.6232 (m-40) REVERT: X 29 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6508 (mttp) REVERT: Y 19 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7836 (tppt) REVERT: Y 49 ASP cc_start: 0.7633 (m-30) cc_final: 0.7366 (m-30) REVERT: Y 111 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: Z 13 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7679 (ttp80) REVERT: a 31 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: b 93 LEU cc_start: 0.2931 (OUTLIER) cc_final: 0.2481 (mp) REVERT: c 33 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7967 (mttt) REVERT: c 81 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5890 (t70) REVERT: d 61 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7226 (mt) REVERT: d 85 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6343 (mttt) REVERT: g 2 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.2508 (mtmt) REVERT: g 19 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6755 (mm) REVERT: g 38 GLN cc_start: 0.6078 (mm-40) cc_final: 0.5561 (tp40) REVERT: i 15 MET cc_start: 0.8064 (mtt) cc_final: 0.7853 (mtp) REVERT: i 53 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7526 (tptm) REVERT: j 45 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7496 (mm-40) REVERT: k 25 LYS cc_start: 0.7123 (ttpp) cc_final: 0.6613 (tptp) REVERT: k 29 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: l 25 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7718 (ptmt) REVERT: m 4 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6656 (mtm180) REVERT: D 9 MET cc_start: 0.5149 (mmt) cc_final: 0.4445 (ptp) REVERT: D 39 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6055 (m90) REVERT: D 95 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6135 (tpt-90) REVERT: D 162 PHE cc_start: 0.6647 (t80) cc_final: 0.6294 (t80) REVERT: D 205 ASP cc_start: 0.4706 (OUTLIER) cc_final: 0.3834 (m-30) REVERT: D 213 TYR cc_start: 0.6709 (m-80) cc_final: 0.6457 (m-80) REVERT: E 8 ASN cc_start: 0.7536 (t0) cc_final: 0.7218 (t0) REVERT: E 135 LYS cc_start: 0.7099 (mtmt) cc_final: 0.6862 (mmpt) REVERT: F 33 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5978 (ptpt) REVERT: F 89 ASN cc_start: 0.7169 (m-40) cc_final: 0.6756 (m110) REVERT: F 104 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6301 (tpm170) REVERT: F 115 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5716 (tmm-80) REVERT: F 128 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.4768 (ptp-110) REVERT: G 64 MET cc_start: 0.7451 (mmt) cc_final: 0.6913 (mmt) REVERT: G 159 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.6111 (mmtt) REVERT: H 14 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: H 21 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6399 (mtt) REVERT: H 91 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6423 (mtm180) REVERT: H 100 SER cc_start: 0.7052 (p) cc_final: 0.6563 (t) REVERT: N 131 LYS cc_start: 0.5733 (mtmt) cc_final: 0.5528 (ptmt) REVERT: N 149 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6015 (tttp) REVERT: P 85 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7889 (mm) REVERT: P 124 GLU cc_start: 0.7228 (tt0) cc_final: 0.6742 (tt0) REVERT: Q 85 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.4931 (mpp80) REVERT: Q 89 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5174 (tp30) REVERT: o 27 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5569 (mm-30) REVERT: o 60 ASP cc_start: 0.7120 (m-30) cc_final: 0.6806 (m-30) REVERT: p 56 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6450 (mmt-90) REVERT: p 109 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5319 (p0) REVERT: r 21 SER cc_start: 0.7494 (m) cc_final: 0.7255 (t) REVERT: r 45 ILE cc_start: 0.7155 (mm) cc_final: 0.6690 (mm) REVERT: r 49 SER cc_start: 0.6802 (OUTLIER) cc_final: 0.6369 (t) REVERT: r 83 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7198 (tt) REVERT: s 6 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7210 (mmt) REVERT: s 11 VAL cc_start: 0.7487 (p) cc_final: 0.7225 (t) REVERT: s 31 ILE cc_start: 0.7200 (mt) cc_final: 0.6913 (tp) REVERT: s 46 LEU cc_start: 0.7476 (mt) cc_final: 0.7144 (mp) REVERT: s 47 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6680 (tttp) REVERT: t 8 THR cc_start: 0.8282 (m) cc_final: 0.8032 (p) REVERT: t 80 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6439 (tm130) REVERT: u 17 TYR cc_start: 0.8154 (m-80) cc_final: 0.7937 (m-80) REVERT: u 25 ARG cc_start: 0.7454 (mtm180) cc_final: 0.7140 (mpp80) REVERT: u 33 ILE cc_start: 0.8115 (mt) cc_final: 0.7831 (mt) REVERT: v 27 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6168 (ptt-90) REVERT: w 34 THR cc_start: 0.6086 (OUTLIER) cc_final: 0.5611 (m) REVERT: x 73 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6401 (mt-10) REVERT: y 85 LYS cc_start: 0.5079 (ptmm) cc_final: 0.4681 (ptmt) REVERT: 5 60 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3611 (mt) REVERT: 5 63 GLU cc_start: 0.3690 (OUTLIER) cc_final: 0.2814 (mm-30) REVERT: 5 69 ARG cc_start: 0.4360 (OUTLIER) cc_final: 0.3504 (ptm160) outliers start: 321 outliers final: 156 residues processed: 1031 average time/residue: 2.1270 time to fit residues: 3127.9344 Evaluate side-chains 957 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 750 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 44 LYS Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 136 MET Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 100 CYS Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 12 GLN Chi-restraints excluded: chain d residue 24 ASN Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain i residue 18 SER Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 53 LYS Chi-restraints excluded: chain j residue 7 GLU Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain s residue 6 MET Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 33 THR Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 35 SER Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 26 SER Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 489 optimal weight: 0.5980 chunk 273 optimal weight: 10.0000 chunk 732 optimal weight: 8.9990 chunk 599 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 881 optimal weight: 9.9990 chunk 952 optimal weight: 7.9990 chunk 785 optimal weight: 0.7980 chunk 874 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 707 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 53 HIS M 115 GLN M 156 ASN M 195 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Z 86 GLN a 61 ASN f 6 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS G 19 ASN ** N 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 GLN Q 32 GLN Q 110 GLN p 81 ASN r 52 GLN v 9 GLN y 52 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 153180 Z= 0.245 Angle : 0.692 28.247 229662 Z= 0.360 Chirality : 0.039 0.414 29358 Planarity : 0.006 0.134 11932 Dihedral : 24.080 177.865 77993 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.85 % Favored : 94.86 % Rotamer: Outliers : 6.73 % Allowed : 19.24 % Favored : 74.04 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.57 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 5214 helix: 0.67 (0.12), residues: 1782 sheet: -1.60 (0.15), residues: 982 loop : -1.28 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 64 HIS 0.006 0.001 HIS 5 56 PHE 0.024 0.002 PHE x 10 TYR 0.019 0.002 TYR Y 32 ARG 0.008 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 800 time to evaluate : 6.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 146 MET cc_start: 0.7932 (mtp) cc_final: 0.7610 (mtp) REVERT: K 272 SER cc_start: 0.5725 (OUTLIER) cc_final: 0.5188 (p) REVERT: L 168 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7020 (tm-30) REVERT: L 177 VAL cc_start: 0.8533 (p) cc_final: 0.8276 (t) REVERT: M 21 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6510 (ptm160) REVERT: M 136 GLN cc_start: 0.7502 (tp40) cc_final: 0.7131 (mm-40) REVERT: O 6 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.6098 (ttpp) REVERT: O 10 VAL cc_start: 0.5945 (OUTLIER) cc_final: 0.5605 (t) REVERT: O 27 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3902 (mtmm) REVERT: O 99 LYS cc_start: 0.6713 (mptp) cc_final: 0.6354 (mtmp) REVERT: O 139 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7489 (tm130) REVERT: R 86 GLN cc_start: 0.7449 (pt0) cc_final: 0.7243 (pt0) REVERT: S 7 MET cc_start: 0.8249 (mmm) cc_final: 0.7716 (mmm) REVERT: S 53 LYS cc_start: 0.6985 (mmtm) cc_final: 0.6582 (mmtt) REVERT: S 106 GLU cc_start: 0.6323 (mp0) cc_final: 0.5890 (mm-30) REVERT: T 1 MET cc_start: 0.7303 (ttp) cc_final: 0.7094 (ttp) REVERT: T 5 THR cc_start: 0.7058 (m) cc_final: 0.6851 (t) REVERT: T 123 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6616 (ttp80) REVERT: W 21 LEU cc_start: 0.8583 (mt) cc_final: 0.8355 (mt) REVERT: W 69 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: X 3 ASN cc_start: 0.6483 (m-40) cc_final: 0.6241 (m-40) REVERT: X 29 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6447 (mttp) REVERT: X 53 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6537 (tpp80) REVERT: Y 19 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7820 (tppt) REVERT: Y 49 ASP cc_start: 0.7496 (m-30) cc_final: 0.7205 (m-30) REVERT: Y 111 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: Y 112 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7052 (tptp) REVERT: Z 13 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7302 (ttp-170) REVERT: Z 40 MET cc_start: 0.8000 (ttt) cc_final: 0.7731 (ttp) REVERT: a 31 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: b 93 LEU cc_start: 0.2895 (OUTLIER) cc_final: 0.2415 (mp) REVERT: c 33 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (mttt) REVERT: c 81 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.5767 (t70) REVERT: d 61 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7155 (mt) REVERT: e 78 LYS cc_start: 0.7596 (mppt) cc_final: 0.7220 (mmtm) REVERT: g 19 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6728 (mm) REVERT: g 38 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5502 (tp40) REVERT: j 45 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7549 (mm-40) REVERT: k 25 LYS cc_start: 0.6964 (ttpp) cc_final: 0.6697 (ttmm) REVERT: l 15 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7983 (mmtp) REVERT: m 4 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7846 (mtt-85) REVERT: m 36 ARG cc_start: 0.7891 (tmt90) cc_final: 0.7635 (ttt-90) REVERT: D 9 MET cc_start: 0.4941 (mmt) cc_final: 0.4276 (ptp) REVERT: D 95 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6050 (tpt-90) REVERT: D 152 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6511 (ttpt) REVERT: D 162 PHE cc_start: 0.6588 (t80) cc_final: 0.6185 (t80) REVERT: F 33 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5949 (ptpt) REVERT: F 89 ASN cc_start: 0.7162 (m-40) cc_final: 0.6811 (m110) REVERT: F 100 ASN cc_start: 0.7212 (t0) cc_final: 0.6906 (t0) REVERT: F 115 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5658 (tmm-80) REVERT: F 128 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4582 (ptp-110) REVERT: F 134 SER cc_start: 0.7550 (p) cc_final: 0.7333 (p) REVERT: F 206 LYS cc_start: 0.6379 (tppp) cc_final: 0.5636 (ttmt) REVERT: G 11 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7181 (mt) REVERT: G 45 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6551 (mtp-110) REVERT: G 64 MET cc_start: 0.7471 (mmt) cc_final: 0.6977 (mmt) REVERT: G 159 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6006 (mmtt) REVERT: H 91 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6412 (mtm180) REVERT: H 100 SER cc_start: 0.6962 (p) cc_final: 0.6537 (t) REVERT: N 30 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6229 (mt) REVERT: N 149 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6089 (tttp) REVERT: P 85 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (mm) REVERT: Q 32 GLN cc_start: 0.5251 (mm110) cc_final: 0.5042 (mm-40) REVERT: Q 85 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.4848 (mpp80) REVERT: Q 89 GLU cc_start: 0.5425 (OUTLIER) cc_final: 0.5088 (tp30) REVERT: o 60 ASP cc_start: 0.7071 (m-30) cc_final: 0.6763 (m-30) REVERT: p 14 LYS cc_start: 0.5535 (OUTLIER) cc_final: 0.5209 (pmmt) REVERT: p 109 ASN cc_start: 0.5748 (OUTLIER) cc_final: 0.5241 (p0) REVERT: q 74 LEU cc_start: 0.7543 (mt) cc_final: 0.7218 (mp) REVERT: r 49 SER cc_start: 0.6577 (OUTLIER) cc_final: 0.6294 (t) REVERT: r 83 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7008 (tp) REVERT: r 93 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.4713 (mmt180) REVERT: r 116 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5332 (tp) REVERT: s 11 VAL cc_start: 0.7489 (p) cc_final: 0.7203 (t) REVERT: s 46 LEU cc_start: 0.7415 (mt) cc_final: 0.7203 (mp) REVERT: s 65 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6273 (ttm110) REVERT: u 25 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7050 (mpp80) REVERT: u 33 ILE cc_start: 0.8154 (mt) cc_final: 0.7832 (mt) REVERT: w 9 LYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4545 (ttpt) REVERT: x 73 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6223 (mt-10) REVERT: y 18 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6946 (ttp80) REVERT: y 36 TYR cc_start: 0.5979 (m-80) cc_final: 0.5671 (m-80) REVERT: y 85 LYS cc_start: 0.5000 (ptmm) cc_final: 0.4689 (ptmt) REVERT: 5 4 ILE cc_start: 0.4988 (mp) cc_final: 0.4444 (tt) REVERT: 5 60 LEU cc_start: 0.4015 (OUTLIER) cc_final: 0.3402 (mt) REVERT: 5 63 GLU cc_start: 0.3567 (OUTLIER) cc_final: 0.2875 (mm-30) outliers start: 292 outliers final: 140 residues processed: 978 average time/residue: 2.0954 time to fit residues: 2935.8435 Evaluate side-chains 920 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 739 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 37 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 870 optimal weight: 2.9990 chunk 662 optimal weight: 10.0000 chunk 457 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 420 optimal weight: 1.9990 chunk 591 optimal weight: 10.0000 chunk 884 optimal weight: 20.0000 chunk 936 optimal weight: 10.0000 chunk 462 optimal weight: 6.9990 chunk 838 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 overall best weight: 6.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN c 40 ASN f 6 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN G 148 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN q 6 GLN r 52 GLN s 4 GLN u 18 GLN v 9 GLN y 52 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 153180 Z= 0.245 Angle : 0.692 28.247 229662 Z= 0.360 Chirality : 0.039 0.414 29358 Planarity : 0.006 0.134 11932 Dihedral : 24.078 177.865 77976 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.85 % Favored : 94.86 % Rotamer: Outliers : 4.24 % Allowed : 23.24 % Favored : 72.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.57 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 5214 helix: 0.67 (0.12), residues: 1782 sheet: -1.60 (0.15), residues: 982 loop : -1.28 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 64 HIS 0.006 0.001 HIS 5 56 PHE 0.024 0.002 PHE x 10 TYR 0.019 0.002 TYR Y 32 ARG 0.008 0.001 ARG W 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 740 time to evaluate : 6.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 146 MET cc_start: 0.7863 (mtp) cc_final: 0.7610 (mtp) REVERT: K 272 SER cc_start: 0.5717 (OUTLIER) cc_final: 0.5187 (p) REVERT: L 168 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7020 (tm-30) REVERT: L 177 VAL cc_start: 0.8533 (p) cc_final: 0.8276 (t) REVERT: M 21 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6510 (ptm160) REVERT: M 136 GLN cc_start: 0.7506 (tp40) cc_final: 0.7131 (mm-40) REVERT: O 6 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6098 (ttpp) REVERT: O 10 VAL cc_start: 0.5951 (OUTLIER) cc_final: 0.5605 (t) REVERT: O 27 LYS cc_start: 0.4125 (OUTLIER) cc_final: 0.3902 (mtmm) REVERT: O 99 LYS cc_start: 0.6708 (mptp) cc_final: 0.6354 (mtmp) REVERT: O 139 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7489 (tm130) REVERT: S 7 MET cc_start: 0.8241 (mmm) cc_final: 0.7716 (mmm) REVERT: S 53 LYS cc_start: 0.6990 (mmtm) cc_final: 0.6583 (mmtt) REVERT: S 106 GLU cc_start: 0.6323 (mp0) cc_final: 0.5890 (mm-30) REVERT: T 1 MET cc_start: 0.7303 (ttp) cc_final: 0.7094 (ttp) REVERT: T 123 ARG cc_start: 0.7099 (ttp80) cc_final: 0.6616 (ttp80) REVERT: W 21 LEU cc_start: 0.8575 (mt) cc_final: 0.8355 (mt) REVERT: W 69 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: X 3 ASN cc_start: 0.6479 (m-40) cc_final: 0.6240 (m-40) REVERT: X 29 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6447 (mttp) REVERT: X 53 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.6537 (tpp80) REVERT: Y 19 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7820 (tppt) REVERT: Y 49 ASP cc_start: 0.7494 (m-30) cc_final: 0.7206 (m-30) REVERT: Y 111 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6454 (tp30) REVERT: Y 112 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7052 (tptp) REVERT: Z 13 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7302 (ttp-170) REVERT: Z 40 MET cc_start: 0.7991 (ttt) cc_final: 0.7731 (ttp) REVERT: a 31 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: b 93 LEU cc_start: 0.2883 (OUTLIER) cc_final: 0.2415 (mp) REVERT: c 33 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7980 (mttt) REVERT: c 81 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.5768 (t70) REVERT: d 61 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7155 (mt) REVERT: e 78 LYS cc_start: 0.7640 (mppt) cc_final: 0.7220 (mmtm) REVERT: g 19 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6728 (mm) REVERT: g 38 GLN cc_start: 0.5978 (mm-40) cc_final: 0.5502 (tp40) REVERT: j 45 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7549 (mm-40) REVERT: k 25 LYS cc_start: 0.6960 (ttpp) cc_final: 0.6697 (ttmm) REVERT: l 15 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7983 (mmtp) REVERT: m 4 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7846 (mtt-85) REVERT: m 36 ARG cc_start: 0.7887 (tmt90) cc_final: 0.7635 (ttt-90) REVERT: D 9 MET cc_start: 0.4920 (mmt) cc_final: 0.4276 (ptp) REVERT: D 95 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.6048 (tpt-90) REVERT: D 152 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6513 (ttpt) REVERT: D 162 PHE cc_start: 0.6597 (t80) cc_final: 0.6183 (t80) REVERT: F 33 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5951 (ptpt) REVERT: F 89 ASN cc_start: 0.7197 (m-40) cc_final: 0.6808 (m110) REVERT: F 100 ASN cc_start: 0.7227 (t0) cc_final: 0.6905 (t0) REVERT: F 115 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5657 (tmm-80) REVERT: F 128 ARG cc_start: 0.5405 (OUTLIER) cc_final: 0.4583 (ptp-110) REVERT: F 134 SER cc_start: 0.7555 (p) cc_final: 0.7333 (p) REVERT: F 196 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5752 (m110) REVERT: F 206 LYS cc_start: 0.6377 (tppp) cc_final: 0.5634 (ttmt) REVERT: G 11 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7181 (mt) REVERT: G 45 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6550 (mtp-110) REVERT: G 64 MET cc_start: 0.7464 (mmt) cc_final: 0.6975 (mmt) REVERT: G 159 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6005 (mmtt) REVERT: H 91 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6412 (mtm180) REVERT: H 100 SER cc_start: 0.6959 (p) cc_final: 0.6537 (t) REVERT: N 30 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6231 (mt) REVERT: N 149 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6101 (tttp) REVERT: P 85 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7951 (mm) REVERT: Q 85 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.4849 (mpp80) REVERT: Q 89 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5088 (tp30) REVERT: o 60 ASP cc_start: 0.7069 (m-30) cc_final: 0.6763 (m-30) REVERT: p 14 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.5209 (pmmt) REVERT: p 109 ASN cc_start: 0.5746 (OUTLIER) cc_final: 0.5241 (p0) REVERT: q 74 LEU cc_start: 0.7542 (mt) cc_final: 0.7218 (mp) REVERT: r 49 SER cc_start: 0.6694 (OUTLIER) cc_final: 0.6294 (t) REVERT: r 83 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7008 (tp) REVERT: r 93 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.4713 (mmt180) REVERT: r 116 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5332 (tp) REVERT: s 11 VAL cc_start: 0.7478 (p) cc_final: 0.7203 (t) REVERT: s 46 LEU cc_start: 0.7433 (mt) cc_final: 0.7203 (mp) REVERT: s 65 ARG cc_start: 0.6542 (ttm170) cc_final: 0.6274 (ttm110) REVERT: u 18 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: u 25 ARG cc_start: 0.7365 (mtm180) cc_final: 0.7049 (mpp80) REVERT: u 33 ILE cc_start: 0.8150 (mt) cc_final: 0.7836 (mt) REVERT: w 9 LYS cc_start: 0.4853 (OUTLIER) cc_final: 0.4545 (ttpt) REVERT: x 73 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6223 (mt-10) REVERT: y 18 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6946 (ttp80) REVERT: y 36 TYR cc_start: 0.5982 (m-80) cc_final: 0.5671 (m-80) REVERT: y 85 LYS cc_start: 0.5000 (ptmm) cc_final: 0.4690 (ptmt) REVERT: 5 4 ILE cc_start: 0.4962 (mp) cc_final: 0.4445 (tt) REVERT: 5 60 LEU cc_start: 0.4006 (OUTLIER) cc_final: 0.3401 (mt) REVERT: 5 63 GLU cc_start: 0.3560 (OUTLIER) cc_final: 0.2874 (mm-30) outliers start: 184 outliers final: 140 residues processed: 860 average time/residue: 2.1751 time to fit residues: 2671.2371 Evaluate side-chains 921 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 738 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 37 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain l residue 15 LYS Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain u residue 18 GLN Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 780 optimal weight: 0.6980 chunk 531 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 697 optimal weight: 20.0000 chunk 386 optimal weight: 9.9990 chunk 799 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 478 optimal weight: 7.9990 chunk 840 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 92 HIS M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 HIS ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN e 57 HIS f 6 GLN g 20 ASN g 36 GLN D 39 HIS P 38 ASN Q 110 GLN r 52 GLN u 18 GLN v 9 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153180 Z= 0.434 Angle : 0.833 29.516 229662 Z= 0.419 Chirality : 0.046 0.377 29358 Planarity : 0.008 0.145 11932 Dihedral : 24.047 179.796 77976 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 7.76 % Allowed : 20.29 % Favored : 71.94 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5214 helix: 0.34 (0.12), residues: 1787 sheet: -1.57 (0.15), residues: 985 loop : -1.40 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 64 HIS 0.009 0.002 HIS F 198 PHE 0.041 0.003 PHE D 184 TYR 0.021 0.003 TYR Y 32 ARG 0.010 0.001 ARG u 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 731 time to evaluate : 6.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: K 146 MET cc_start: 0.7865 (mtp) cc_final: 0.7615 (mtp) REVERT: L 1 MET cc_start: 0.5401 (mpt) cc_final: 0.5030 (mpt) REVERT: L 168 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 21 ARG cc_start: 0.7112 (ptp-170) cc_final: 0.6632 (ptm160) REVERT: M 136 GLN cc_start: 0.7377 (tp40) cc_final: 0.7008 (mm-40) REVERT: M 162 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: O 6 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5999 (ttpp) REVERT: O 10 VAL cc_start: 0.5978 (OUTLIER) cc_final: 0.5634 (t) REVERT: O 88 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6589 (pt0) REVERT: O 99 LYS cc_start: 0.6768 (mptp) cc_final: 0.6514 (mtmp) REVERT: S 7 MET cc_start: 0.8302 (mmm) cc_final: 0.7829 (mmm) REVERT: S 53 LYS cc_start: 0.6945 (mmtm) cc_final: 0.6566 (mmtt) REVERT: T 1 MET cc_start: 0.7327 (ttp) cc_final: 0.7119 (ttp) REVERT: T 13 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7606 (mptm) REVERT: U 40 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6128 (mtm180) REVERT: V 33 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8423 (tp) REVERT: W 21 LEU cc_start: 0.8592 (mt) cc_final: 0.8368 (mt) REVERT: W 69 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: X 3 ASN cc_start: 0.6555 (m-40) cc_final: 0.6312 (m-40) REVERT: X 29 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6557 (mttp) REVERT: Y 49 ASP cc_start: 0.7641 (m-30) cc_final: 0.7393 (m-30) REVERT: Y 111 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: Z 13 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7624 (ttp80) REVERT: Z 20 VAL cc_start: 0.7373 (p) cc_final: 0.7081 (t) REVERT: a 31 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6649 (mm-40) REVERT: a 62 ASP cc_start: 0.6730 (m-30) cc_final: 0.6506 (m-30) REVERT: b 93 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2421 (mp) REVERT: c 33 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7933 (mttp) REVERT: c 39 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7433 (mp) REVERT: c 81 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.5924 (t70) REVERT: d 61 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7269 (mt) REVERT: d 85 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6383 (mttt) REVERT: e 78 LYS cc_start: 0.7527 (mppt) cc_final: 0.7117 (mmtm) REVERT: f 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6405 (ptp-170) REVERT: g 19 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 25 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: g 38 GLN cc_start: 0.5994 (mm-40) cc_final: 0.5514 (tp40) REVERT: j 45 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7425 (mm110) REVERT: k 29 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: l 25 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7697 (ptmt) REVERT: m 4 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 95 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6104 (tpt-90) REVERT: D 152 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6409 (ttpp) REVERT: D 162 PHE cc_start: 0.6659 (t80) cc_final: 0.6253 (t80) REVERT: D 220 THR cc_start: 0.7152 (p) cc_final: 0.6760 (m) REVERT: E 8 ASN cc_start: 0.7562 (t0) cc_final: 0.7230 (t0) REVERT: F 33 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5933 (ptpt) REVERT: F 89 ASN cc_start: 0.7207 (m-40) cc_final: 0.6758 (m110) REVERT: F 115 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5666 (tmm-80) REVERT: F 128 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.4684 (ptp-110) REVERT: F 206 LYS cc_start: 0.6496 (tppp) cc_final: 0.5698 (ttmt) REVERT: G 11 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7160 (mt) REVERT: G 64 MET cc_start: 0.7450 (mmt) cc_final: 0.6909 (mmt) REVERT: G 159 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6090 (mmtt) REVERT: H 14 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6100 (mp10) REVERT: H 21 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6286 (mtt) REVERT: H 75 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5453 (mm-30) REVERT: H 91 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6428 (mtm180) REVERT: H 100 SER cc_start: 0.7002 (p) cc_final: 0.6580 (t) REVERT: N 30 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6373 (mt) REVERT: N 149 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6056 (ttmp) REVERT: P 85 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7862 (mm) REVERT: P 124 GLU cc_start: 0.7138 (tt0) cc_final: 0.6700 (tt0) REVERT: Q 4 ASN cc_start: 0.4017 (p0) cc_final: 0.3771 (p0) REVERT: Q 85 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.4770 (mpp80) REVERT: Q 89 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5150 (tp30) REVERT: o 7 ARG cc_start: 0.5996 (mpt-90) cc_final: 0.5439 (mpt-90) REVERT: o 60 ASP cc_start: 0.7147 (m-30) cc_final: 0.6920 (m-30) REVERT: o 68 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7209 (mtt-85) REVERT: p 14 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5334 (pmmt) REVERT: p 109 ASN cc_start: 0.5712 (p0) cc_final: 0.5232 (p0) REVERT: r 49 SER cc_start: 0.6325 (OUTLIER) cc_final: 0.5927 (t) REVERT: r 83 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7171 (tt) REVERT: s 11 VAL cc_start: 0.7542 (p) cc_final: 0.7257 (t) REVERT: t 8 THR cc_start: 0.8024 (m) cc_final: 0.7779 (p) REVERT: t 80 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6725 (mm-40) REVERT: u 25 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7077 (mpp80) REVERT: u 33 ILE cc_start: 0.8163 (mt) cc_final: 0.7836 (mt) REVERT: u 45 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4106 (mp0) REVERT: v 27 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6106 (ptt-90) REVERT: w 9 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4781 (tmtp) REVERT: w 34 THR cc_start: 0.5926 (p) cc_final: 0.5622 (m) REVERT: x 73 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6392 (mt-10) REVERT: y 40 GLU cc_start: 0.5464 (tt0) cc_final: 0.4762 (tt0) REVERT: y 85 LYS cc_start: 0.5115 (ptmm) cc_final: 0.4757 (ptmt) REVERT: 5 60 LEU cc_start: 0.4055 (OUTLIER) cc_final: 0.3771 (tm) REVERT: 5 63 GLU cc_start: 0.3569 (OUTLIER) cc_final: 0.2924 (mm-30) REVERT: 5 69 ARG cc_start: 0.4150 (OUTLIER) cc_final: 0.3293 (ptm160) outliers start: 337 outliers final: 193 residues processed: 941 average time/residue: 2.0857 time to fit residues: 2808.8497 Evaluate side-chains 965 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 720 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 162 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 48 MET Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 28 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 ARG Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 31 ASN Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 315 optimal weight: 2.9990 chunk 843 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 549 optimal weight: 0.0980 chunk 231 optimal weight: 10.0000 chunk 937 optimal weight: 0.0870 chunk 778 optimal weight: 9.9990 chunk 434 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 492 optimal weight: 3.9990 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN d 12 GLN f 6 GLN F 40 GLN F 196 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN s 66 GLN v 9 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153180 Z= 0.434 Angle : 0.833 29.516 229662 Z= 0.419 Chirality : 0.046 0.377 29358 Planarity : 0.008 0.145 11932 Dihedral : 24.047 179.796 77976 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 5.69 % Allowed : 22.85 % Favored : 71.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5214 helix: 0.34 (0.12), residues: 1787 sheet: -1.57 (0.15), residues: 985 loop : -1.40 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 64 HIS 0.009 0.002 HIS F 198 PHE 0.041 0.003 PHE D 184 TYR 0.021 0.003 TYR Y 32 ARG 0.010 0.001 ARG u 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 721 time to evaluate : 6.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: K 146 MET cc_start: 0.7871 (mtp) cc_final: 0.7615 (mtp) REVERT: L 1 MET cc_start: 0.5391 (mpt) cc_final: 0.5029 (mpt) REVERT: L 168 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 21 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6632 (ptm160) REVERT: M 136 GLN cc_start: 0.7377 (tp40) cc_final: 0.7009 (mm-40) REVERT: M 162 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: O 6 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.5998 (ttpp) REVERT: O 10 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5635 (t) REVERT: O 88 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: O 99 LYS cc_start: 0.6767 (mptp) cc_final: 0.6514 (mtmp) REVERT: S 7 MET cc_start: 0.8296 (mmm) cc_final: 0.7825 (mmm) REVERT: S 53 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6563 (mmtt) REVERT: T 1 MET cc_start: 0.7324 (ttp) cc_final: 0.7119 (ttp) REVERT: T 13 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7606 (mptm) REVERT: U 40 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6128 (mtm180) REVERT: V 33 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8422 (tp) REVERT: W 21 LEU cc_start: 0.8579 (mt) cc_final: 0.8367 (mt) REVERT: W 69 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: X 3 ASN cc_start: 0.6549 (m-40) cc_final: 0.6312 (m-40) REVERT: X 29 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6551 (mttp) REVERT: Y 49 ASP cc_start: 0.7642 (m-30) cc_final: 0.7393 (m-30) REVERT: Y 111 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: Z 20 VAL cc_start: 0.7371 (p) cc_final: 0.7069 (t) REVERT: a 31 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6649 (mm-40) REVERT: b 93 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2420 (mp) REVERT: c 33 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7933 (mttp) REVERT: c 39 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (mp) REVERT: c 81 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.5924 (t70) REVERT: d 61 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7267 (mt) REVERT: d 85 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6384 (mttt) REVERT: e 78 LYS cc_start: 0.7524 (mppt) cc_final: 0.7118 (mmtm) REVERT: f 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6405 (ptp-170) REVERT: g 19 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 25 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: g 38 GLN cc_start: 0.5997 (mm-40) cc_final: 0.5514 (tp40) REVERT: j 45 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7415 (mm110) REVERT: k 29 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: l 25 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (ptmt) REVERT: m 4 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 95 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6103 (tpt-90) REVERT: D 152 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6406 (ttpp) REVERT: D 162 PHE cc_start: 0.6664 (t80) cc_final: 0.6250 (t80) REVERT: D 220 THR cc_start: 0.7169 (p) cc_final: 0.6755 (m) REVERT: E 8 ASN cc_start: 0.7542 (t0) cc_final: 0.7234 (t0) REVERT: F 33 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5933 (ptpt) REVERT: F 89 ASN cc_start: 0.7202 (m-40) cc_final: 0.6758 (m110) REVERT: F 115 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5666 (tmm-80) REVERT: F 128 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4684 (ptp-110) REVERT: F 206 LYS cc_start: 0.6501 (tppp) cc_final: 0.5699 (ttmt) REVERT: G 11 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7162 (mt) REVERT: G 64 MET cc_start: 0.7451 (mmt) cc_final: 0.6909 (mmt) REVERT: G 159 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6089 (mmtt) REVERT: H 14 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: H 21 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6286 (mtt) REVERT: H 75 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5453 (mm-30) REVERT: H 91 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6429 (mtm180) REVERT: H 100 SER cc_start: 0.7000 (p) cc_final: 0.6580 (t) REVERT: N 30 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6374 (mt) REVERT: N 149 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6057 (ttmp) REVERT: P 85 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (mm) REVERT: P 124 GLU cc_start: 0.7141 (tt0) cc_final: 0.6701 (tt0) REVERT: Q 85 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.4771 (mpp80) REVERT: Q 89 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5145 (tp30) REVERT: o 7 ARG cc_start: 0.5808 (mpt-90) cc_final: 0.5439 (mpt-90) REVERT: o 60 ASP cc_start: 0.7145 (m-30) cc_final: 0.6918 (m-30) REVERT: o 68 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: p 14 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5334 (pmmt) REVERT: p 109 ASN cc_start: 0.5714 (p0) cc_final: 0.5232 (p0) REVERT: r 49 SER cc_start: 0.6325 (OUTLIER) cc_final: 0.5928 (t) REVERT: r 83 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7168 (tt) REVERT: s 11 VAL cc_start: 0.7544 (p) cc_final: 0.7257 (t) REVERT: t 8 THR cc_start: 0.8027 (m) cc_final: 0.7780 (p) REVERT: t 80 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6725 (mm-40) REVERT: u 25 ARG cc_start: 0.7391 (mtm180) cc_final: 0.7078 (mpp80) REVERT: u 33 ILE cc_start: 0.8165 (mt) cc_final: 0.7835 (mt) REVERT: u 45 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4106 (mp0) REVERT: v 27 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6106 (ptt-90) REVERT: w 9 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4782 (tmtp) REVERT: w 34 THR cc_start: 0.5910 (p) cc_final: 0.5622 (m) REVERT: x 73 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6395 (mt-10) REVERT: y 40 GLU cc_start: 0.5456 (tt0) cc_final: 0.4762 (tt0) REVERT: y 85 LYS cc_start: 0.5117 (ptmm) cc_final: 0.4757 (ptmt) REVERT: 5 60 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3772 (tm) REVERT: 5 63 GLU cc_start: 0.3571 (OUTLIER) cc_final: 0.2925 (mm-30) REVERT: 5 69 ARG cc_start: 0.4160 (OUTLIER) cc_final: 0.3291 (ptm160) outliers start: 247 outliers final: 193 residues processed: 881 average time/residue: 2.0757 time to fit residues: 2624.8837 Evaluate side-chains 967 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 722 time to evaluate : 5.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 162 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 48 MET Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 28 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 ARG Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 31 ASN Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 903 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 534 optimal weight: 0.6980 chunk 684 optimal weight: 20.0000 chunk 530 optimal weight: 0.9980 chunk 789 optimal weight: 6.9990 chunk 523 optimal weight: 1.9990 chunk 933 optimal weight: 7.9990 chunk 584 optimal weight: 20.0000 chunk 569 optimal weight: 0.9990 chunk 431 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN d 12 GLN f 6 GLN F 196 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN v 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153180 Z= 0.434 Angle : 0.833 29.516 229662 Z= 0.419 Chirality : 0.046 0.377 29358 Planarity : 0.008 0.145 11932 Dihedral : 24.047 179.796 77976 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 5.69 % Allowed : 22.92 % Favored : 71.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5214 helix: 0.34 (0.12), residues: 1787 sheet: -1.57 (0.15), residues: 985 loop : -1.40 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 64 HIS 0.009 0.002 HIS F 198 PHE 0.041 0.003 PHE D 184 TYR 0.021 0.003 TYR Y 32 ARG 0.010 0.001 ARG u 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 723 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: K 146 MET cc_start: 0.7871 (mtp) cc_final: 0.7615 (mtp) REVERT: L 1 MET cc_start: 0.5390 (mpt) cc_final: 0.5029 (mpt) REVERT: L 168 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 21 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6632 (ptm160) REVERT: M 136 GLN cc_start: 0.7377 (tp40) cc_final: 0.7008 (mm-40) REVERT: M 162 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: O 6 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5998 (ttpp) REVERT: O 10 VAL cc_start: 0.5979 (OUTLIER) cc_final: 0.5635 (t) REVERT: O 88 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: O 99 LYS cc_start: 0.6767 (mptp) cc_final: 0.6514 (mtmp) REVERT: S 7 MET cc_start: 0.8294 (mmm) cc_final: 0.7825 (mmm) REVERT: S 53 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6563 (mmtt) REVERT: T 1 MET cc_start: 0.7325 (ttp) cc_final: 0.7119 (ttp) REVERT: T 13 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (mptm) REVERT: U 40 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6128 (mtm180) REVERT: V 33 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (tp) REVERT: W 21 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt) REVERT: W 69 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: X 3 ASN cc_start: 0.6549 (m-40) cc_final: 0.6312 (m-40) REVERT: X 29 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6551 (mttp) REVERT: Y 49 ASP cc_start: 0.7641 (m-30) cc_final: 0.7392 (m-30) REVERT: Y 111 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6622 (tp30) REVERT: Z 20 VAL cc_start: 0.7378 (p) cc_final: 0.7069 (t) REVERT: a 31 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6648 (mm-40) REVERT: b 93 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2420 (mp) REVERT: c 33 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (mttp) REVERT: c 39 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7431 (mp) REVERT: c 81 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.5924 (t70) REVERT: d 61 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7267 (mt) REVERT: d 85 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6384 (mttt) REVERT: e 78 LYS cc_start: 0.7525 (mppt) cc_final: 0.7118 (mmtm) REVERT: f 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6404 (ptp-170) REVERT: g 19 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 25 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: g 38 GLN cc_start: 0.5998 (mm-40) cc_final: 0.5514 (tp40) REVERT: j 45 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7415 (mm110) REVERT: k 29 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: l 25 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (ptmt) REVERT: m 4 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 95 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6102 (tpt-90) REVERT: D 152 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6405 (ttpp) REVERT: D 162 PHE cc_start: 0.6660 (t80) cc_final: 0.6250 (t80) REVERT: D 220 THR cc_start: 0.7162 (p) cc_final: 0.6757 (m) REVERT: E 8 ASN cc_start: 0.7545 (t0) cc_final: 0.7233 (t0) REVERT: F 33 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5933 (ptpt) REVERT: F 89 ASN cc_start: 0.7203 (m-40) cc_final: 0.6757 (m110) REVERT: F 115 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5665 (tmm-80) REVERT: F 128 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4684 (ptp-110) REVERT: F 206 LYS cc_start: 0.6501 (tppp) cc_final: 0.5700 (ttmt) REVERT: G 11 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7158 (mt) REVERT: G 64 MET cc_start: 0.7450 (mmt) cc_final: 0.6910 (mmt) REVERT: G 159 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6089 (mmtt) REVERT: H 14 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: H 21 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6286 (mtt) REVERT: H 75 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5453 (mm-30) REVERT: H 91 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6428 (mtm180) REVERT: H 100 SER cc_start: 0.7000 (p) cc_final: 0.6581 (t) REVERT: N 30 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6374 (mt) REVERT: N 149 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6057 (ttmp) REVERT: P 85 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (mm) REVERT: P 124 GLU cc_start: 0.7141 (tt0) cc_final: 0.6701 (tt0) REVERT: Q 85 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4771 (mpp80) REVERT: Q 89 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5145 (tp30) REVERT: o 7 ARG cc_start: 0.5808 (mpt-90) cc_final: 0.5439 (mpt-90) REVERT: o 60 ASP cc_start: 0.7144 (m-30) cc_final: 0.6918 (m-30) REVERT: o 68 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: p 14 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5333 (pmmt) REVERT: p 109 ASN cc_start: 0.5713 (p0) cc_final: 0.5232 (p0) REVERT: r 49 SER cc_start: 0.6326 (OUTLIER) cc_final: 0.5928 (t) REVERT: r 83 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7168 (tt) REVERT: s 11 VAL cc_start: 0.7544 (p) cc_final: 0.7257 (t) REVERT: t 8 THR cc_start: 0.8028 (m) cc_final: 0.7780 (p) REVERT: t 80 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6725 (mm-40) REVERT: u 25 ARG cc_start: 0.7391 (mtm180) cc_final: 0.7078 (mpp80) REVERT: u 33 ILE cc_start: 0.8165 (mt) cc_final: 0.7835 (mt) REVERT: u 45 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4106 (mp0) REVERT: v 27 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6106 (ptt-90) REVERT: w 9 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4782 (tmtp) REVERT: w 34 THR cc_start: 0.5910 (p) cc_final: 0.5622 (m) REVERT: x 73 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6395 (mt-10) REVERT: y 40 GLU cc_start: 0.5456 (tt0) cc_final: 0.4762 (tt0) REVERT: y 85 LYS cc_start: 0.5117 (ptmm) cc_final: 0.4757 (ptmt) REVERT: 5 60 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3770 (tm) REVERT: 5 63 GLU cc_start: 0.3573 (OUTLIER) cc_final: 0.2924 (mm-30) REVERT: 5 69 ARG cc_start: 0.4158 (OUTLIER) cc_final: 0.3289 (ptm160) outliers start: 247 outliers final: 193 residues processed: 883 average time/residue: 2.1157 time to fit residues: 2674.0469 Evaluate side-chains 966 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 721 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 162 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 48 MET Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 28 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 ARG Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 31 ASN Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 577 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 557 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 593 optimal weight: 20.0000 chunk 636 optimal weight: 10.0000 chunk 461 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 734 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN d 12 GLN f 6 GLN F 196 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN v 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153180 Z= 0.434 Angle : 0.833 29.516 229662 Z= 0.419 Chirality : 0.046 0.377 29358 Planarity : 0.008 0.145 11932 Dihedral : 24.047 179.796 77976 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 5.69 % Allowed : 22.92 % Favored : 71.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5214 helix: 0.34 (0.12), residues: 1787 sheet: -1.57 (0.15), residues: 985 loop : -1.40 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 64 HIS 0.009 0.002 HIS F 198 PHE 0.041 0.003 PHE D 184 TYR 0.021 0.003 TYR Y 32 ARG 0.010 0.001 ARG u 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 722 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: K 146 MET cc_start: 0.7871 (mtp) cc_final: 0.7615 (mtp) REVERT: L 1 MET cc_start: 0.5390 (mpt) cc_final: 0.5029 (mpt) REVERT: L 168 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 21 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6632 (ptm160) REVERT: M 136 GLN cc_start: 0.7377 (tp40) cc_final: 0.7008 (mm-40) REVERT: M 162 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: O 6 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5998 (ttpp) REVERT: O 10 VAL cc_start: 0.5978 (OUTLIER) cc_final: 0.5635 (t) REVERT: O 88 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: O 99 LYS cc_start: 0.6767 (mptp) cc_final: 0.6514 (mtmp) REVERT: S 7 MET cc_start: 0.8294 (mmm) cc_final: 0.7825 (mmm) REVERT: S 53 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6563 (mmtt) REVERT: T 1 MET cc_start: 0.7325 (ttp) cc_final: 0.7119 (ttp) REVERT: T 13 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (mptm) REVERT: U 40 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6128 (mtm180) REVERT: V 33 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (tp) REVERT: W 21 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt) REVERT: W 69 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: X 3 ASN cc_start: 0.6549 (m-40) cc_final: 0.6312 (m-40) REVERT: X 29 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6551 (mttp) REVERT: Y 49 ASP cc_start: 0.7642 (m-30) cc_final: 0.7393 (m-30) REVERT: Y 111 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: Z 20 VAL cc_start: 0.7378 (p) cc_final: 0.7069 (t) REVERT: a 31 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6649 (mm-40) REVERT: b 93 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2420 (mp) REVERT: c 33 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (mttp) REVERT: c 39 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7431 (mp) REVERT: c 81 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.5924 (t70) REVERT: d 61 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7267 (mt) REVERT: d 85 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6384 (mttt) REVERT: e 78 LYS cc_start: 0.7525 (mppt) cc_final: 0.7117 (mmtm) REVERT: f 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6405 (ptp-170) REVERT: g 19 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 25 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: g 38 GLN cc_start: 0.5998 (mm-40) cc_final: 0.5514 (tp40) REVERT: j 45 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7415 (mm110) REVERT: k 29 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: l 25 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (ptmt) REVERT: m 4 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 95 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6102 (tpt-90) REVERT: D 152 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6405 (ttpp) REVERT: D 162 PHE cc_start: 0.6660 (t80) cc_final: 0.6250 (t80) REVERT: D 220 THR cc_start: 0.7164 (p) cc_final: 0.6757 (m) REVERT: E 8 ASN cc_start: 0.7545 (t0) cc_final: 0.7233 (t0) REVERT: F 33 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5933 (ptpt) REVERT: F 89 ASN cc_start: 0.7202 (m-40) cc_final: 0.6757 (m110) REVERT: F 115 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5665 (tmm-80) REVERT: F 128 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4684 (ptp-110) REVERT: F 206 LYS cc_start: 0.6502 (tppp) cc_final: 0.5700 (ttmt) REVERT: G 11 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7158 (mt) REVERT: G 64 MET cc_start: 0.7450 (mmt) cc_final: 0.6910 (mmt) REVERT: G 159 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6089 (mmtt) REVERT: H 14 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: H 21 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6286 (mtt) REVERT: H 75 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5453 (mm-30) REVERT: H 91 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6428 (mtm180) REVERT: H 100 SER cc_start: 0.7000 (p) cc_final: 0.6581 (t) REVERT: N 30 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6374 (mt) REVERT: N 149 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6057 (ttmp) REVERT: P 85 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (mm) REVERT: P 124 GLU cc_start: 0.7141 (tt0) cc_final: 0.6701 (tt0) REVERT: Q 85 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4771 (mpp80) REVERT: Q 89 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5145 (tp30) REVERT: o 7 ARG cc_start: 0.5808 (mpt-90) cc_final: 0.5439 (mpt-90) REVERT: o 60 ASP cc_start: 0.7144 (m-30) cc_final: 0.6918 (m-30) REVERT: o 68 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: p 14 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5333 (pmmt) REVERT: p 109 ASN cc_start: 0.5713 (p0) cc_final: 0.5232 (p0) REVERT: r 49 SER cc_start: 0.6326 (OUTLIER) cc_final: 0.5928 (t) REVERT: r 83 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7168 (tt) REVERT: s 11 VAL cc_start: 0.7544 (p) cc_final: 0.7257 (t) REVERT: t 8 THR cc_start: 0.8028 (m) cc_final: 0.7780 (p) REVERT: t 80 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6725 (mm-40) REVERT: u 25 ARG cc_start: 0.7391 (mtm180) cc_final: 0.7078 (mpp80) REVERT: u 33 ILE cc_start: 0.8165 (mt) cc_final: 0.7835 (mt) REVERT: u 45 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4106 (mp0) REVERT: v 27 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6106 (ptt-90) REVERT: w 9 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4782 (tmtp) REVERT: w 34 THR cc_start: 0.5910 (p) cc_final: 0.5622 (m) REVERT: x 73 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6395 (mt-10) REVERT: y 40 GLU cc_start: 0.5456 (tt0) cc_final: 0.4762 (tt0) REVERT: y 85 LYS cc_start: 0.5118 (ptmm) cc_final: 0.4758 (ptmt) REVERT: 5 60 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3770 (tm) REVERT: 5 63 GLU cc_start: 0.3572 (OUTLIER) cc_final: 0.2924 (mm-30) REVERT: 5 69 ARG cc_start: 0.4155 (OUTLIER) cc_final: 0.3289 (ptm160) outliers start: 247 outliers final: 193 residues processed: 882 average time/residue: 2.1073 time to fit residues: 2660.8836 Evaluate side-chains 966 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 721 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 162 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 48 MET Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 28 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 ARG Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 31 ASN Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 849 optimal weight: 9.9990 chunk 894 optimal weight: 1.9990 chunk 816 optimal weight: 6.9990 chunk 870 optimal weight: 0.2980 chunk 523 optimal weight: 6.9990 chunk 379 optimal weight: 20.0000 chunk 683 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 786 optimal weight: 8.9990 chunk 823 optimal weight: 2.9990 chunk 867 optimal weight: 6.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 72 ASN Z 86 GLN d 12 GLN f 6 GLN F 196 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN v 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153180 Z= 0.434 Angle : 0.833 29.516 229662 Z= 0.419 Chirality : 0.046 0.377 29358 Planarity : 0.008 0.145 11932 Dihedral : 24.047 179.796 77976 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 5.69 % Allowed : 22.92 % Favored : 71.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5214 helix: 0.34 (0.12), residues: 1787 sheet: -1.57 (0.15), residues: 985 loop : -1.40 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 64 HIS 0.009 0.002 HIS F 198 PHE 0.041 0.003 PHE D 184 TYR 0.021 0.003 TYR Y 32 ARG 0.010 0.001 ARG u 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 722 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: K 146 MET cc_start: 0.7871 (mtp) cc_final: 0.7615 (mtp) REVERT: L 1 MET cc_start: 0.5390 (mpt) cc_final: 0.5029 (mpt) REVERT: L 168 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 21 ARG cc_start: 0.7107 (ptp-170) cc_final: 0.6632 (ptm160) REVERT: M 136 GLN cc_start: 0.7377 (tp40) cc_final: 0.7008 (mm-40) REVERT: M 162 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: O 6 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5998 (ttpp) REVERT: O 10 VAL cc_start: 0.5978 (OUTLIER) cc_final: 0.5635 (t) REVERT: O 88 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: O 99 LYS cc_start: 0.6767 (mptp) cc_final: 0.6514 (mtmp) REVERT: S 7 MET cc_start: 0.8294 (mmm) cc_final: 0.7825 (mmm) REVERT: S 53 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6563 (mmtt) REVERT: T 1 MET cc_start: 0.7325 (ttp) cc_final: 0.7119 (ttp) REVERT: T 13 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7605 (mptm) REVERT: U 40 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6128 (mtm180) REVERT: V 33 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (tp) REVERT: W 21 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt) REVERT: W 69 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: X 3 ASN cc_start: 0.6549 (m-40) cc_final: 0.6312 (m-40) REVERT: X 29 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6551 (mttp) REVERT: Y 49 ASP cc_start: 0.7641 (m-30) cc_final: 0.7392 (m-30) REVERT: Y 111 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6622 (tp30) REVERT: Z 20 VAL cc_start: 0.7378 (p) cc_final: 0.7069 (t) REVERT: a 31 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6648 (mm-40) REVERT: b 93 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2420 (mp) REVERT: c 33 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (mttp) REVERT: c 39 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7431 (mp) REVERT: c 81 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.5924 (t70) REVERT: d 61 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7267 (mt) REVERT: d 85 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6384 (mttt) REVERT: e 78 LYS cc_start: 0.7525 (mppt) cc_final: 0.7118 (mmtm) REVERT: f 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6404 (ptp-170) REVERT: g 19 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 25 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: g 38 GLN cc_start: 0.5998 (mm-40) cc_final: 0.5514 (tp40) REVERT: j 45 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7415 (mm110) REVERT: k 29 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: l 25 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (ptmt) REVERT: m 4 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 95 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6102 (tpt-90) REVERT: D 152 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6405 (ttpp) REVERT: D 162 PHE cc_start: 0.6660 (t80) cc_final: 0.6250 (t80) REVERT: D 220 THR cc_start: 0.7164 (p) cc_final: 0.6757 (m) REVERT: E 8 ASN cc_start: 0.7545 (t0) cc_final: 0.7233 (t0) REVERT: F 33 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5933 (ptpt) REVERT: F 89 ASN cc_start: 0.7202 (m-40) cc_final: 0.6757 (m110) REVERT: F 115 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5665 (tmm-80) REVERT: F 128 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4684 (ptp-110) REVERT: F 206 LYS cc_start: 0.6502 (tppp) cc_final: 0.5700 (ttmt) REVERT: G 11 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7158 (mt) REVERT: G 64 MET cc_start: 0.7450 (mmt) cc_final: 0.6910 (mmt) REVERT: G 159 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6089 (mmtt) REVERT: H 14 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: H 21 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6286 (mtt) REVERT: H 75 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5453 (mm-30) REVERT: H 91 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6428 (mtm180) REVERT: H 100 SER cc_start: 0.7000 (p) cc_final: 0.6581 (t) REVERT: N 30 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6374 (mt) REVERT: N 149 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6057 (ttmp) REVERT: P 85 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (mm) REVERT: P 124 GLU cc_start: 0.7141 (tt0) cc_final: 0.6701 (tt0) REVERT: Q 85 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4771 (mpp80) REVERT: Q 89 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5145 (tp30) REVERT: o 7 ARG cc_start: 0.5808 (mpt-90) cc_final: 0.5439 (mpt-90) REVERT: o 60 ASP cc_start: 0.7144 (m-30) cc_final: 0.6918 (m-30) REVERT: o 68 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: p 14 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5333 (pmmt) REVERT: p 109 ASN cc_start: 0.5713 (p0) cc_final: 0.5232 (p0) REVERT: r 49 SER cc_start: 0.6326 (OUTLIER) cc_final: 0.5928 (t) REVERT: r 83 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7168 (tt) REVERT: s 11 VAL cc_start: 0.7544 (p) cc_final: 0.7257 (t) REVERT: t 8 THR cc_start: 0.8028 (m) cc_final: 0.7780 (p) REVERT: t 80 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6725 (mm-40) REVERT: u 25 ARG cc_start: 0.7391 (mtm180) cc_final: 0.7078 (mpp80) REVERT: u 33 ILE cc_start: 0.8165 (mt) cc_final: 0.7835 (mt) REVERT: u 45 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4106 (mp0) REVERT: v 27 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6106 (ptt-90) REVERT: w 9 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4782 (tmtp) REVERT: w 34 THR cc_start: 0.5910 (p) cc_final: 0.5622 (m) REVERT: x 73 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6395 (mt-10) REVERT: y 40 GLU cc_start: 0.5456 (tt0) cc_final: 0.4762 (tt0) REVERT: y 85 LYS cc_start: 0.5118 (ptmm) cc_final: 0.4757 (ptmt) REVERT: 5 60 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3770 (tm) REVERT: 5 63 GLU cc_start: 0.3571 (OUTLIER) cc_final: 0.2924 (mm-30) REVERT: 5 69 ARG cc_start: 0.4155 (OUTLIER) cc_final: 0.3289 (ptm160) outliers start: 247 outliers final: 193 residues processed: 882 average time/residue: 2.1025 time to fit residues: 2655.0963 Evaluate side-chains 966 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 721 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 162 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 GLU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 116 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 69 ASP Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 112 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 39 ILE Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 48 MET Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain e residue 81 SER Chi-restraints excluded: chain f residue 2 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 28 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 40 SER Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 68 ARG Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 88 MET Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 14 LYS Chi-restraints excluded: chain p residue 26 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain q residue 115 SER Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 49 SER Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 74 SER Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 93 ARG Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 34 VAL Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain s residue 100 SER Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 80 GLN Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain w residue 9 LYS Chi-restraints excluded: chain w residue 31 ASN Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 31 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain x residue 45 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain y residue 69 LYS Chi-restraints excluded: chain 5 residue 29 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 47 ARG Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 571 optimal weight: 0.6980 chunk 920 optimal weight: 0.6980 chunk 561 optimal weight: 0.9980 chunk 436 optimal weight: 0.0770 chunk 639 optimal weight: 9.9990 chunk 965 optimal weight: 0.9980 chunk 888 optimal weight: 3.9990 chunk 768 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 593 optimal weight: 20.0000 chunk 471 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 ASN Z 86 GLN b 72 GLN f 6 GLN g 36 GLN F 196 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN Q 110 GLN v 9 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 153180 Z= 0.159 Angle : 0.658 30.520 229662 Z= 0.343 Chirality : 0.037 0.452 29358 Planarity : 0.006 0.124 11932 Dihedral : 24.026 177.270 77976 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 3.92 % Allowed : 24.65 % Favored : 71.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 5214 helix: 0.88 (0.12), residues: 1789 sheet: -1.40 (0.15), residues: 1020 loop : -1.09 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP U 64 HIS 0.007 0.001 HIS q 77 PHE 0.027 0.002 PHE x 10 TYR 0.025 0.002 TYR a 38 ARG 0.013 0.001 ARG o 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10428 Ramachandran restraints generated. 5214 Oldfield, 0 Emsley, 5214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 795 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6577 (mt0) REVERT: K 146 MET cc_start: 0.7903 (mtp) cc_final: 0.7691 (mtp) REVERT: K 272 SER cc_start: 0.5619 (t) cc_final: 0.5101 (p) REVERT: L 168 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: M 1 MET cc_start: 0.4688 (ptm) cc_final: 0.3877 (ppp) REVERT: M 21 ARG cc_start: 0.7029 (ptp-170) cc_final: 0.6561 (ptm160) REVERT: M 136 GLN cc_start: 0.7365 (tp40) cc_final: 0.7011 (mm-40) REVERT: O 99 LYS cc_start: 0.6712 (mptp) cc_final: 0.6390 (mtmp) REVERT: S 7 MET cc_start: 0.8186 (mmm) cc_final: 0.7641 (mmm) REVERT: S 53 LYS cc_start: 0.7053 (mmtm) cc_final: 0.6627 (mmtt) REVERT: S 71 ARG cc_start: 0.7015 (mmt90) cc_final: 0.6601 (mmm-85) REVERT: S 106 GLU cc_start: 0.6387 (mp0) cc_final: 0.5917 (mm-30) REVERT: T 123 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6599 (ttp80) REVERT: X 3 ASN cc_start: 0.6572 (m-40) cc_final: 0.6370 (m-40) REVERT: X 115 ASN cc_start: 0.4324 (OUTLIER) cc_final: 0.3723 (m-40) REVERT: Y 19 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7906 (tppt) REVERT: Y 49 ASP cc_start: 0.7520 (m-30) cc_final: 0.7234 (m-30) REVERT: Z 34 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5711 (mm-30) REVERT: a 31 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: b 93 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2354 (mp) REVERT: c 31 SER cc_start: 0.7158 (t) cc_final: 0.6709 (p) REVERT: c 33 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (mttt) REVERT: c 81 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.5742 (t70) REVERT: d 61 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7142 (mt) REVERT: d 85 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6477 (mttt) REVERT: e 78 LYS cc_start: 0.7595 (mppt) cc_final: 0.7215 (mmtm) REVERT: g 19 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6689 (mm) REVERT: g 38 GLN cc_start: 0.5942 (mm-40) cc_final: 0.5493 (tp40) REVERT: j 45 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7413 (mm110) REVERT: k 29 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7054 (mt0) REVERT: l 15 LYS cc_start: 0.8181 (tppt) cc_final: 0.7975 (mmtp) REVERT: m 36 ARG cc_start: 0.7927 (ptm-80) cc_final: 0.7667 (ttt180) REVERT: D 9 MET cc_start: 0.5006 (mmt) cc_final: 0.4268 (ptp) REVERT: D 28 LYS cc_start: 0.6406 (tppt) cc_final: 0.5768 (tttm) REVERT: D 95 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5944 (tpt-90) REVERT: D 152 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6479 (ttpp) REVERT: D 162 PHE cc_start: 0.6601 (t80) cc_final: 0.6189 (t80) REVERT: F 33 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5805 (ptpt) REVERT: F 89 ASN cc_start: 0.7134 (m-40) cc_final: 0.6783 (m110) REVERT: F 100 ASN cc_start: 0.7157 (t0) cc_final: 0.6893 (t0) REVERT: F 128 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.4600 (ptp-110) REVERT: F 179 GLU cc_start: 0.4847 (OUTLIER) cc_final: 0.4411 (pm20) REVERT: F 198 HIS cc_start: 0.5362 (p90) cc_final: 0.5124 (p90) REVERT: F 206 LYS cc_start: 0.6367 (tppp) cc_final: 0.5698 (ttmt) REVERT: G 11 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7202 (mt) REVERT: G 64 MET cc_start: 0.7488 (mmt) cc_final: 0.6991 (mmt) REVERT: G 159 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6007 (mmtt) REVERT: H 14 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6067 (mp10) REVERT: H 91 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6290 (mtm180) REVERT: H 100 SER cc_start: 0.6986 (p) cc_final: 0.6529 (t) REVERT: N 30 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6232 (mt) REVERT: N 111 ARG cc_start: 0.3998 (mtp85) cc_final: 0.3765 (mtp85) REVERT: N 149 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6136 (tttp) REVERT: Q 85 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4727 (mpp80) REVERT: Q 89 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5044 (tp30) REVERT: p 59 THR cc_start: 0.7531 (p) cc_final: 0.7217 (p) REVERT: p 109 ASN cc_start: 0.5524 (p0) cc_final: 0.5113 (p0) REVERT: q 74 LEU cc_start: 0.7554 (mt) cc_final: 0.7233 (mp) REVERT: r 49 SER cc_start: 0.6324 (p) cc_final: 0.5908 (t) REVERT: r 83 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6901 (tp) REVERT: s 11 VAL cc_start: 0.7415 (p) cc_final: 0.7204 (m) REVERT: u 25 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6825 (mpp80) REVERT: u 33 ILE cc_start: 0.8143 (mt) cc_final: 0.7831 (mt) REVERT: u 45 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.4094 (mp0) REVERT: w 61 ARG cc_start: 0.7139 (mtm-85) cc_final: 0.6869 (mtt90) REVERT: x 73 GLU cc_start: 0.6392 (mt-10) cc_final: 0.6183 (mt-10) REVERT: y 18 ARG cc_start: 0.7150 (ttp80) cc_final: 0.6936 (ttp80) REVERT: y 85 LYS cc_start: 0.4916 (ptmm) cc_final: 0.4538 (ptmt) REVERT: 5 4 ILE cc_start: 0.4780 (mp) cc_final: 0.4276 (tt) REVERT: 5 60 LEU cc_start: 0.4075 (OUTLIER) cc_final: 0.3497 (mt) REVERT: 5 63 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.2716 (mm-30) outliers start: 170 outliers final: 83 residues processed: 897 average time/residue: 2.1818 time to fit residues: 2789.4895 Evaluate side-chains 852 residues out of total 4342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 740 time to evaluate : 5.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 166 LYS Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 76 THR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain Z residue 19 THR Chi-restraints excluded: chain Z residue 99 THR Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 81 ASP Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 85 LYS Chi-restraints excluded: chain e residue 41 ARG Chi-restraints excluded: chain g residue 19 LEU Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain k residue 29 GLN Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 111 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 42 ASP Chi-restraints excluded: chain r residue 75 MET Chi-restraints excluded: chain r residue 83 LEU Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain t residue 14 GLU Chi-restraints excluded: chain u residue 45 GLU Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 20 SER Chi-restraints excluded: chain v residue 46 VAL Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 610 optimal weight: 20.0000 chunk 818 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 769 optimal weight: 0.0770 chunk 322 optimal weight: 8.9990 chunk 790 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN V 9 GLN ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN Y 72 ASN Z 86 GLN f 6 GLN g 31 GLN g 36 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 110 GLN r 52 GLN s 66 GLN y 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103249 restraints weight = 213668.389| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 0.69 r_work: 0.3030 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 153180 Z= 0.371 Angle : 0.765 27.955 229662 Z= 0.387 Chirality : 0.043 0.377 29358 Planarity : 0.007 0.141 11932 Dihedral : 23.918 178.962 77973 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 3.46 % Allowed : 25.64 % Favored : 70.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.11), residues: 5214 helix: 0.65 (0.12), residues: 1796 sheet: -1.37 (0.16), residues: 993 loop : -1.21 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 64 HIS 0.012 0.002 HIS q 77 PHE 0.041 0.003 PHE x 10 TYR 0.023 0.003 TYR F 65 ARG 0.014 0.001 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40114.71 seconds wall clock time: 697 minutes 58.64 seconds (41878.64 seconds total)