Starting phenix.real_space_refine on Sun Apr 14 22:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8htz_35020/04_2024/8htz_35020_updated.pdb" } resolution = 2.4 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= -0.000 sd= 0.009 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 K 1 8.98 5 P 4556 5.49 5 Mg 317 5.21 5 S 150 5.16 5 C 71071 2.51 5 N 26418 2.21 5 O 39406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 167": "OD1" <-> "OD2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "n GLU 55": "OE1" <-> "OE2" Residue "n ASP 93": "OD1" <-> "OD2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "p ASP 102": "OD1" <-> "OD2" Residue "q PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 94": "OD1" <-> "OD2" Residue "u ASP 76": "OD1" <-> "OD2" Residue "y ASP 40": "OD1" <-> "OD2" Residue "0 GLU 51": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141919 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 81, 'rna3p': 10, 'rna3p_pur': 742, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" 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 breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 139, 'rna3p': 16, 'rna3p_pur': 1318, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" 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: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" 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: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" 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: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" 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: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" 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: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" 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: "s" 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: "t" 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: "u" 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: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: "w" 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: "x" 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: "y" 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: "z" 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: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" 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: "2" 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: "3" 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: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "V" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "W" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "X" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1687 Classifications: {'RNA': 78} Modifications used: {'rna2p': 1, 'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 11, 'rna3p': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Unusual residues: {' K': 1, ' MG': 94} Classifications: {'undetermined': 95} Link IDs: {None: 94} Chain: "N" 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: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Unusual residues: {' MG': 208} Classifications: {'undetermined': 208} Link IDs: {None: 207} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" 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: "X" 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} Time building chain proxies: 59.45, per 1000 atoms: 0.42 Number of scatterers: 141919 At special positions: 0 Unit cell: (253.521, 236.122, 250.207, 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) K 1 19.00 S 150 16.00 P 4556 15.00 Mg 317 11.99 O 39406 8.00 N 26418 7.00 C 71071 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.75 Conformation dependent library (CDL) restraints added in 7.9 seconds 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10260 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: 169 helices and 71 sheets defined 38.8% alpha, 20.0% beta 1593 base pairs and 2381 stacking pairs defined. Time for finding SS restraints: 79.76 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 4.174A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.589A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.732A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 5.130A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.075A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.737A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.909A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 removed outlier: 3.745A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.595A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.114A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.510A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.505A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.940A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.594A pdb=" N GLY D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.711A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.808A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 4.039A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.723A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.837A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 5.188A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 44 " --> pdb=" O HIS D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.972A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.570A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 Proline residue: F 19 - end of helix removed outlier: 3.893A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.779A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.788A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.589A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.613A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 153 removed outlier: 3.645A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.979A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.552A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.059A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.653A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 93 through 104 removed outlier: 3.977A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.715A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.713A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 4.127A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 64 removed outlier: 4.357A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.507A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 4.794A pdb=" N ARG N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.368A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.042A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.507A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.125A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.494A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.851A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.538A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.063A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.835A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.960A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.728A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.931A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.958A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 6.250A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 105 removed outlier: 4.303A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL d 104 " --> pdb=" O LEU d 100 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS d 105 " --> pdb=" O PHE d 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 105' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.509A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 3.568A pdb=" N PHE e 158 " --> pdb=" O ASP e 154 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 20 removed outlier: 5.085A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.062A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 5.053A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.765A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 4.394A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 7 removed outlier: 3.693A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 81 removed outlier: 4.764A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.320A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.573A pdb=" N GLN h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 29 through 34' Processing helix chain 'i' and resid 24 through 38 Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.169A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 123 removed outlier: 3.962A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.631A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.726A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.692A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.774A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.890A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 removed outlier: 3.613A pdb=" N GLY k 139 " --> pdb=" O ILE k 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.103A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 57 removed outlier: 4.253A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.663A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.371A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.174A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.538A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 3.841A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 removed outlier: 3.651A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.677A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.582A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.690A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.702A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 73 removed outlier: 3.816A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 4.254A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 Processing helix chain 's' and resid 3 through 11 removed outlier: 4.318A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.781A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.854A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.611A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.290A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.854A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.567A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.506A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 18 Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.105A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.644A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.750A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 4.822A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.689A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 89 through 92 Processing sheet with id= 3, first strand: chain 'C' and resid 54 through 59 removed outlier: 3.593A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.591A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.712A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.716A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.953A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.977A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.598A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR F 59 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 5.822A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.259A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.557A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 removed outlier: 4.761A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 35 through 38 removed outlier: 4.248A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE J 6 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 11 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 42 through 52 removed outlier: 5.229A pdb=" N LEU J 71 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.504A pdb=" N ARG K 106 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.153A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.228A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.652A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.715A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'Q' and resid 56 through 59 removed outlier: 7.176A pdb=" N GLY Q 56 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA Q 82 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.873A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.845A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.784A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.201A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.250A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 3 through 9 removed outlier: 4.274A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.701A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.512A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.823A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.556A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 117 through 120 removed outlier: 3.731A pdb=" N LYS e 185 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.551A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU f 152 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 15 through 20 removed outlier: 5.941A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 94 through 99 removed outlier: 3.630A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.171A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY g 161 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'h' and resid 1 through 4 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 41, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.398A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.288A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.508A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.787A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.895A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 33 through 37 removed outlier: 4.914A pdb=" N ARG m 103 " --> pdb=" O ASN m 107 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY m 101 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA m 111 " --> pdb=" O LYS m 99 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS m 99 " --> pdb=" O ALA m 111 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE m 113 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE m 97 " --> pdb=" O ILE m 113 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU m 115 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR m 95 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'n' and resid 49 through 52 Processing sheet with id= 49, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.477A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.733A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.662A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.135A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 54, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.558A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.269A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 2 through 8 removed outlier: 6.863A pdb=" N VAL r 106 " --> pdb=" O THR r 72 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'r' and resid 73 through 79 removed outlier: 4.761A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 80 through 88 removed outlier: 4.046A pdb=" N THR r 100 " --> pdb=" O PRO r 80 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 's' and resid 12 through 15 removed outlier: 5.075A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY s 75 " --> pdb=" O LYS s 68 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 40 through 45 removed outlier: 4.799A pdb=" N ASN t 40 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 83 through 86 Processing sheet with id= 62, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.890A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.308A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 65, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.588A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 34 through 41 removed outlier: 3.724A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.241A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '0' and resid 19 through 24 removed outlier: 6.166A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '2' and resid 22 through 25 removed outlier: 5.727A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '3' and resid 1 through 5 removed outlier: 6.607A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '4' and resid 11 through 15 removed outlier: 3.618A pdb=" N MET 4 22 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) 1908 hydrogen bonds defined for protein. 5634 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4006 hydrogen bonds 6272 hydrogen bond angles 0 basepair planarities 1593 basepair parallelities 2381 stacking parallelities Total time for adding SS restraints: 299.20 Time building geometry restraints manager: 64.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 13954 1.31 - 1.45: 69376 1.45 - 1.59: 61425 1.59 - 1.73: 8902 1.73 - 1.86: 264 Bond restraints: 153921 Sorted by residual: bond pdb=" C4 B8H X 54 " pdb=" C5 B8H X 54 " ideal model delta sigma weight residual 1.834 1.482 0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" N3 B8H X 54 " pdb=" C4 B8H X 54 " ideal model delta sigma weight residual 1.136 1.485 -0.349 2.00e-02 2.50e+03 3.04e+02 bond pdb=" C5 B8H X 54 " pdb=" C6 B8H X 54 " ideal model delta sigma weight residual 1.135 1.443 -0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.452 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.446 -0.291 2.00e-02 2.50e+03 2.12e+02 ... (remaining 153916 not shown) Histogram of bond angle deviations from ideal: 97.97 - 107.29: 31203 107.29 - 116.61: 105962 116.61 - 125.92: 77505 125.92 - 135.24: 15671 135.24 - 144.55: 3 Bond angle restraints: 230344 Sorted by residual: angle pdb=" C1' 2MA V 38 " pdb=" N9 2MA V 38 " pdb=" C8 2MA V 38 " ideal model delta sigma weight residual 106.32 144.55 -38.23 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 141.46 -35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C1' 2MA V 38 " pdb=" N9 2MA V 38 " pdb=" C4 2MA V 38 " ideal model delta sigma weight residual 138.88 107.64 31.24 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 111.15 27.73 3.00e+00 1.11e-01 8.55e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 131.70 -21.63 3.00e+00 1.11e-01 5.20e+01 ... (remaining 230339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 87047 35.72 - 71.45: 10114 71.45 - 107.17: 1276 107.17 - 142.90: 12 142.90 - 178.62: 12 Dihedral angle restraints: 98461 sinusoidal: 82556 harmonic: 15905 Sorted by residual: dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual -180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 dihedral pdb=" O4' C X 70 " pdb=" C1' C X 70 " pdb=" N1 C X 70 " pdb=" C2 C X 70 " ideal model delta sinusoidal sigma weight residual -160.00 -2.28 -157.72 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 51.63 148.37 1 1.50e+01 4.44e-03 7.90e+01 ... (remaining 98458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 26965 0.068 - 0.136: 2154 0.136 - 0.204: 174 0.204 - 0.273: 18 0.273 - 0.341: 9 Chirality restraints: 29320 Sorted by residual: chirality pdb=" CA MEQ d 150 " pdb=" N MEQ d 150 " pdb=" C MEQ d 150 " pdb=" CB MEQ d 150 " both_signs ideal model delta sigma weight residual False 2.38 2.72 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C2' 3TD a1915 " pdb=" C3' 3TD a1915 " pdb=" O2' 3TD a1915 " pdb=" C1' 3TD a1915 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA MS6 l 82 " pdb=" C MS6 l 82 " pdb=" CB MS6 l 82 " pdb=" N1 MS6 l 82 " both_signs ideal model delta sigma weight residual False 2.50 2.80 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 29317 not shown) Planarity restraints: 12255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.068 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' 2MG A1516 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.619 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.663 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.157 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.996 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.946 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.047 2.00e-02 2.50e+03 6.05e-01 8.22e+03 pdb=" C4' 2MG A1207 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.715 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.610 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.205 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.932 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.205 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " 0.058 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMC a2498 " 0.441 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " 0.626 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " -0.636 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " -0.176 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " 0.971 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " 0.224 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " -0.916 2.00e-02 2.50e+03 ... (remaining 12252 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.50: 760 2.50 - 3.16: 106673 3.16 - 3.82: 345134 3.82 - 4.48: 479665 4.48 - 5.14: 627495 Nonbonded interactions: 1559727 Sorted by model distance: nonbonded pdb=" OP2 A A1500 " pdb="MG MG A1654 " model vdw 1.846 2.170 nonbonded pdb=" OP1 U a 120 " pdb="MG MG a6003 " model vdw 1.869 2.170 nonbonded pdb=" OP2 A a1010 " pdb="MG MG a6102 " model vdw 1.887 2.170 nonbonded pdb=" OP1 G a2502 " pdb="MG MG a6053 " model vdw 1.897 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6124 " model vdw 1.899 2.170 ... (remaining 1559722 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 36.350 Check model and map are aligned: 1.580 Set scattering table: 1.050 Process input model: 613.270 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 682.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.006 0.352 153921 Z= 0.338 Angle : 0.695 38.234 230344 Z= 0.348 Chirality : 0.039 0.341 29320 Planarity : 0.022 0.608 12255 Dihedral : 22.724 178.620 88201 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.14 (0.11), residues: 5474 helix: 0.80 (0.12), residues: 1832 sheet: -0.33 (0.15), residues: 1097 loop : -0.56 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 23 HIS 0.011 0.001 HIS M 14 PHE 0.031 0.002 PHE F 78 TYR 0.032 0.002 TYR h 25 ARG 0.013 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 984 time to evaluate : 6.239 Fit side-chains REVERT: E 147 MET cc_start: 0.7549 (ttp) cc_final: 0.7016 (ttp) REVERT: G 116 MET cc_start: 0.7867 (tpt) cc_final: 0.7664 (tpt) REVERT: M 21 SER cc_start: 0.7399 (m) cc_final: 0.7193 (m) outliers start: 0 outliers final: 0 residues processed: 984 average time/residue: 2.4469 time to fit residues: 3297.5971 Evaluate side-chains 862 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 862 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 10.0000 chunk 748 optimal weight: 0.0020 chunk 415 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 505 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 774 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 470 optimal weight: 40.0000 chunk 576 optimal weight: 10.0000 chunk 897 optimal weight: 0.9990 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS J 56 HIS K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN N 49 GLN O 35 GLN O 40 GLN c 70 ASN c 115 GLN d 32 ASN i 128 ASN j 3 GLN l 60 GLN n 19 GLN o 7 GLN o 41 GLN s 92 ASN t 40 ASN u 24 ASN w 6 GLN x 25 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.0443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 153921 Z= 0.286 Angle : 0.774 18.108 230344 Z= 0.408 Chirality : 0.041 0.340 29320 Planarity : 0.008 0.144 12255 Dihedral : 23.152 178.823 77173 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 10.21 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.20 (0.11), residues: 5474 helix: 0.73 (0.12), residues: 1897 sheet: -0.27 (0.15), residues: 1108 loop : -0.66 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.013 0.002 HIS M 14 PHE 0.022 0.002 PHE F 78 TYR 0.021 0.002 TYR p 32 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 865 time to evaluate : 6.260 Fit side-chains REVERT: B 205 ASP cc_start: 0.4432 (OUTLIER) cc_final: 0.4149 (m-30) REVERT: E 16 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.6344 (pp) REVERT: F 102 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.4193 (mpt) REVERT: G 79 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5616 (ttt90) REVERT: G 116 MET cc_start: 0.7823 (tpt) cc_final: 0.7510 (tpt) REVERT: G 118 LEU cc_start: 0.7956 (tp) cc_final: 0.7752 (tt) REVERT: L 108 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.5808 (mppt) REVERT: Q 40 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6305 (mmp-170) REVERT: c 251 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: j 4 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6996 (mt-10) outliers start: 95 outliers final: 50 residues processed: 906 average time/residue: 2.4301 time to fit residues: 3031.0117 Evaluate side-chains 892 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 834 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 225 MET Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 61 ARG Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 82 MET Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain 0 residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 498 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 746 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 898 optimal weight: 0.0470 chunk 970 optimal weight: 0.9990 chunk 800 optimal weight: 8.9990 chunk 891 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 721 optimal weight: 9.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 40 GLN T 13 GLN T 78 ASN U 9 ASN c 70 ASN c 115 GLN i 128 ASN j 3 GLN l 60 GLN n 19 GLN o 7 GLN ** o 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN u 24 ASN w 6 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 153921 Z= 0.177 Angle : 0.656 15.855 230344 Z= 0.358 Chirality : 0.036 0.368 29320 Planarity : 0.007 0.135 12255 Dihedral : 23.016 178.120 77173 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 12.36 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5474 helix: 1.07 (0.12), residues: 1890 sheet: -0.22 (0.15), residues: 1120 loop : -0.59 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 248 HIS 0.008 0.001 HIS F 11 PHE 0.015 0.002 PHE r 75 TYR 0.016 0.002 TYR p 32 ARG 0.009 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 869 time to evaluate : 6.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.4904 (tp30) REVERT: D 104 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5495 (mtt90) REVERT: E 16 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6250 (pp) REVERT: F 102 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.4162 (mpt) REVERT: G 79 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5630 (ttt90) REVERT: G 116 MET cc_start: 0.7737 (tpt) cc_final: 0.7421 (tpt) REVERT: I 88 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5039 (mpp) REVERT: L 9 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6849 (ttm110) REVERT: S 48 THR cc_start: 0.6339 (OUTLIER) cc_final: 0.6006 (m) REVERT: T 24 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5797 (mtt-85) REVERT: c 251 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7206 (tp40) REVERT: d 128 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6775 (mmp80) REVERT: f 7 TYR cc_start: 0.6443 (t80) cc_final: 0.6197 (t80) REVERT: j 4 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: l 55 ARG cc_start: 0.7245 (ttp80) cc_final: 0.7019 (ttm-80) REVERT: o 63 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7852 (pttm) outliers start: 101 outliers final: 57 residues processed: 918 average time/residue: 2.3827 time to fit residues: 3023.0806 Evaluate side-chains 910 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 841 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain 0 residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 20.0000 chunk 675 optimal weight: 0.3980 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 428 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 902 optimal weight: 5.9990 chunk 955 optimal weight: 10.0000 chunk 471 optimal weight: 40.0000 chunk 854 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 overall best weight: 6.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS G 148 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 35 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 ASN c 70 ASN c 115 GLN i 128 ASN j 3 GLN l 60 GLN o 7 GLN o 10 GLN o 41 GLN t 40 ASN u 24 ASN w 6 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 153921 Z= 0.303 Angle : 0.783 17.532 230344 Z= 0.411 Chirality : 0.042 0.340 29320 Planarity : 0.008 0.146 12255 Dihedral : 23.100 179.129 77173 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.15 % Allowed : 14.30 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5474 helix: 0.81 (0.12), residues: 1901 sheet: -0.29 (0.15), residues: 1113 loop : -0.66 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.011 0.002 HIS M 14 PHE 0.022 0.002 PHE d 118 TYR 0.022 0.002 TYR p 32 ARG 0.011 0.001 ARG p 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 854 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6073 (mtt) REVERT: B 52 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.4817 (tp30) REVERT: B 205 ASP cc_start: 0.4696 (OUTLIER) cc_final: 0.4319 (m-30) REVERT: D 104 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5551 (mtt90) REVERT: E 16 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.6420 (pp) REVERT: F 102 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.4832 (mpt) REVERT: G 79 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5588 (ttt90) REVERT: G 116 MET cc_start: 0.7735 (tpt) cc_final: 0.7396 (tpt) REVERT: H 31 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6208 (mmpt) REVERT: I 88 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5125 (mpp) REVERT: L 9 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6845 (ttm110) REVERT: L 108 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5867 (mppt) REVERT: N 53 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7176 (ptp-170) REVERT: O 6 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: c 251 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: f 7 TYR cc_start: 0.6501 (t80) cc_final: 0.6214 (t80) REVERT: g 86 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6610 (tttt) REVERT: i 85 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7593 (mmtm) REVERT: j 4 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: l 75 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: o 63 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7843 (pttm) REVERT: p 111 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: s 9 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7248 (mptt) REVERT: t 27 ASN cc_start: 0.6579 (OUTLIER) cc_final: 0.6371 (p0) outliers start: 144 outliers final: 81 residues processed: 932 average time/residue: 2.4438 time to fit residues: 3151.9721 Evaluate side-chains 939 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 837 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 85 LYS Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 9 LYS Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 27 ASN Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 795 optimal weight: 7.9990 chunk 542 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 711 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 814 optimal weight: 8.9990 chunk 660 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 487 optimal weight: 30.0000 chunk 857 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS G 148 ASN K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN c 115 GLN j 3 GLN l 60 GLN o 10 GLN t 40 ASN w 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 153921 Z= 0.269 Angle : 0.748 16.146 230344 Z= 0.397 Chirality : 0.040 0.344 29320 Planarity : 0.007 0.142 12255 Dihedral : 23.071 178.734 77173 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 3.39 % Allowed : 15.27 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5474 helix: 0.84 (0.12), residues: 1898 sheet: -0.33 (0.15), residues: 1116 loop : -0.66 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.010 0.002 HIS M 14 PHE 0.019 0.002 PHE d 118 TYR 0.020 0.002 TYR p 32 ARG 0.011 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 857 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6079 (mtt) REVERT: B 52 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.4783 (tp30) REVERT: B 205 ASP cc_start: 0.4763 (OUTLIER) cc_final: 0.4428 (m-30) REVERT: D 104 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5522 (mtt90) REVERT: D 178 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.4921 (mtm) REVERT: E 16 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6372 (pp) REVERT: F 14 GLN cc_start: 0.5605 (OUTLIER) cc_final: 0.4122 (mp-120) REVERT: F 102 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.4912 (mpt) REVERT: G 79 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5336 (ttt90) REVERT: G 116 MET cc_start: 0.7740 (tpt) cc_final: 0.7393 (tpt) REVERT: H 31 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6182 (mmpt) REVERT: I 88 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5165 (mpp) REVERT: I 89 GLU cc_start: 0.6408 (tt0) cc_final: 0.6126 (tt0) REVERT: L 9 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6868 (ttm110) REVERT: L 108 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.5951 (mppt) REVERT: N 53 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6793 (ptp-170) REVERT: c 251 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: d 13 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8331 (ttm170) REVERT: f 7 TYR cc_start: 0.6405 (t80) cc_final: 0.6127 (t80) REVERT: i 85 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (mmtm) REVERT: j 4 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: l 75 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: o 63 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7861 (pttm) REVERT: p 111 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: r 92 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7352 (ttp80) REVERT: s 9 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7186 (mptt) REVERT: v 83 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: y 21 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7683 (ptmt) REVERT: 1 25 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8180 (pptt) outliers start: 155 outliers final: 95 residues processed: 946 average time/residue: 2.3916 time to fit residues: 3130.0729 Evaluate side-chains 959 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 839 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 189 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 85 LYS Chi-restraints excluded: chain i residue 128 ASN Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 9 LYS Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 21 LYS Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 1.9990 chunk 860 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 955 optimal weight: 8.9990 chunk 793 optimal weight: 20.0000 chunk 442 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 501 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS G 148 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 35 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN c 115 GLN j 3 GLN l 60 GLN m 18 GLN o 10 GLN o 41 GLN t 27 ASN t 40 ASN w 6 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 153921 Z= 0.248 Angle : 0.729 16.068 230344 Z= 0.390 Chirality : 0.039 0.349 29320 Planarity : 0.007 0.141 12255 Dihedral : 23.066 178.616 77173 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 3.50 % Allowed : 15.99 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5474 helix: 0.88 (0.12), residues: 1897 sheet: -0.33 (0.15), residues: 1116 loop : -0.66 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.008 0.001 HIS M 14 PHE 0.022 0.002 PHE F 78 TYR 0.020 0.002 TYR p 32 ARG 0.012 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 840 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6083 (mtt) REVERT: B 52 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.4769 (tp30) REVERT: B 205 ASP cc_start: 0.4755 (OUTLIER) cc_final: 0.4424 (m-30) REVERT: D 104 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5525 (mtt90) REVERT: D 128 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.3967 (ttt90) REVERT: D 178 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4894 (mtm) REVERT: E 16 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6367 (pp) REVERT: F 14 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.4015 (mp-120) REVERT: G 79 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5362 (ttt90) REVERT: G 116 MET cc_start: 0.7744 (tpt) cc_final: 0.7383 (tpt) REVERT: H 31 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6183 (mmpt) REVERT: I 88 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5149 (mpp) REVERT: I 89 GLU cc_start: 0.6409 (tt0) cc_final: 0.6167 (tt0) REVERT: L 9 ARG cc_start: 0.7157 (mtm-85) cc_final: 0.6879 (ttm110) REVERT: N 53 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6786 (ptp-170) REVERT: O 6 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: R 30 LYS cc_start: 0.7306 (mmtp) cc_final: 0.6722 (pptt) REVERT: S 48 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.6169 (m) REVERT: c 251 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: d 13 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: d 28 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: f 7 TYR cc_start: 0.6391 (t80) cc_final: 0.6102 (t80) REVERT: i 85 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7579 (mmtm) REVERT: j 4 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: k 13 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6936 (mptt) REVERT: l 75 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: o 63 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7882 (pttm) REVERT: p 111 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6654 (tp30) REVERT: r 92 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7350 (ttp80) REVERT: v 83 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6535 (pt0) REVERT: y 21 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7651 (ptmt) REVERT: 1 25 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8181 (pptt) REVERT: 3 24 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6622 (ptp-170) outliers start: 160 outliers final: 104 residues processed: 935 average time/residue: 2.3937 time to fit residues: 3093.7893 Evaluate side-chains 967 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 835 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 189 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 85 LYS Chi-restraints excluded: chain i residue 128 ASN Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain m residue 74 GLU Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 21 LYS Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 24 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 7.9990 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 952 optimal weight: 1.9990 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS G 148 ASN K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN c 115 GLN e 115 GLN j 3 GLN l 60 GLN m 18 GLN o 10 GLN o 41 GLN t 40 ASN w 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 153921 Z= 0.363 Angle : 0.855 19.702 230344 Z= 0.442 Chirality : 0.045 0.330 29320 Planarity : 0.008 0.150 12255 Dihedral : 23.171 179.185 77173 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 3.76 % Allowed : 16.40 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 5474 helix: 0.59 (0.12), residues: 1890 sheet: -0.37 (0.15), residues: 1108 loop : -0.78 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.012 0.002 HIS M 14 PHE 0.025 0.003 PHE d 118 TYR 0.023 0.003 TYR p 32 ARG 0.012 0.001 ARG p 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 872 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.6469 (ptp) cc_final: 0.6087 (mtt) REVERT: B 52 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.4851 (tp30) REVERT: B 136 MET cc_start: 0.3386 (ttt) cc_final: 0.3161 (ttm) REVERT: C 93 ASP cc_start: 0.5718 (OUTLIER) cc_final: 0.5095 (m-30) REVERT: D 104 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5549 (mtt90) REVERT: D 128 ARG cc_start: 0.5075 (OUTLIER) cc_final: 0.3990 (ttt90) REVERT: D 178 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.4888 (mtm) REVERT: F 11 HIS cc_start: 0.7177 (t-90) cc_final: 0.6924 (t70) REVERT: F 14 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.3566 (mp-120) REVERT: F 102 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.4766 (mpt) REVERT: G 13 LEU cc_start: 0.6777 (tp) cc_final: 0.6429 (tp) REVERT: G 79 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5183 (ttt90) REVERT: G 116 MET cc_start: 0.7753 (tpt) cc_final: 0.7391 (tpt) REVERT: H 31 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6225 (mmpt) REVERT: H 96 MET cc_start: 0.6965 (ptp) cc_final: 0.6476 (ttp) REVERT: I 88 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5234 (mpp) REVERT: I 89 GLU cc_start: 0.6477 (tt0) cc_final: 0.6209 (tt0) REVERT: J 7 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.4697 (mpt-90) REVERT: L 9 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6874 (ttm110) REVERT: N 53 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6369 (ptp-170) REVERT: O 84 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6180 (ttp80) REVERT: R 30 LYS cc_start: 0.7308 (mmtp) cc_final: 0.7098 (mmpt) REVERT: c 251 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7438 (tp40) REVERT: d 13 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8308 (ttm170) REVERT: d 28 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: f 7 TYR cc_start: 0.6406 (t80) cc_final: 0.6121 (t80) REVERT: i 85 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7581 (mmtm) REVERT: j 4 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: l 75 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: o 63 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7874 (pttm) REVERT: p 111 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: r 92 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7387 (ttp80) REVERT: s 9 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7250 (mptt) REVERT: 3 24 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7097 (ptp-170) outliers start: 172 outliers final: 112 residues processed: 976 average time/residue: 2.4087 time to fit residues: 3257.3391 Evaluate side-chains 986 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 850 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 189 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 167 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 85 LYS Chi-restraints excluded: chain i residue 128 ASN Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 9 LYS Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 589 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 568 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 605 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 470 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 748 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN F 17 GLN F 46 GLN F 55 HIS G 148 ASN K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 35 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN c 115 GLN e 115 GLN e 136 GLN g 104 ASN j 3 GLN l 60 GLN m 18 GLN o 10 GLN o 41 GLN t 27 ASN t 40 ASN w 6 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 153921 Z= 0.403 Angle : 0.905 20.697 230344 Z= 0.463 Chirality : 0.047 0.340 29320 Planarity : 0.009 0.153 12255 Dihedral : 23.219 179.636 77173 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 4.22 % Allowed : 16.80 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5474 helix: 0.41 (0.11), residues: 1883 sheet: -0.42 (0.15), residues: 1103 loop : -0.85 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP w 39 HIS 0.013 0.002 HIS M 14 PHE 0.027 0.003 PHE d 118 TYR 0.023 0.003 TYR p 32 ARG 0.014 0.001 ARG p 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 864 time to evaluate : 6.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.4877 (tp30) REVERT: B 136 MET cc_start: 0.3343 (ttt) cc_final: 0.3127 (ttm) REVERT: C 93 ASP cc_start: 0.5706 (OUTLIER) cc_final: 0.5129 (m-30) REVERT: D 91 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5153 (tp) REVERT: D 104 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.5543 (mtt90) REVERT: D 128 ARG cc_start: 0.5099 (OUTLIER) cc_final: 0.4023 (ttt90) REVERT: D 178 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4933 (mtm) REVERT: F 11 HIS cc_start: 0.7248 (t-90) cc_final: 0.6838 (t70) REVERT: F 14 GLN cc_start: 0.5714 (OUTLIER) cc_final: 0.2959 (mp10) REVERT: F 102 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.4711 (mpt) REVERT: G 13 LEU cc_start: 0.6853 (tp) cc_final: 0.6632 (tp) REVERT: G 79 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5143 (ttt90) REVERT: G 116 MET cc_start: 0.7766 (tpt) cc_final: 0.7382 (tpt) REVERT: H 31 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6236 (mmpt) REVERT: H 96 MET cc_start: 0.7017 (ptp) cc_final: 0.6523 (ttp) REVERT: I 88 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5227 (mpp) REVERT: L 9 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.6890 (ttm110) REVERT: N 53 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6314 (ptp-170) REVERT: O 84 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6149 (ttp80) REVERT: R 30 LYS cc_start: 0.7373 (mmtp) cc_final: 0.7134 (mmpt) REVERT: c 251 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7424 (tp40) REVERT: d 13 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8471 (ttm170) REVERT: d 28 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: f 11 GLU cc_start: 0.5784 (mp0) cc_final: 0.5543 (mm-30) REVERT: i 85 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7581 (mmtm) REVERT: i 96 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6341 (pmt170) REVERT: j 4 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: l 55 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6741 (ttm-80) REVERT: l 75 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: o 63 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7880 (pttm) REVERT: p 111 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: r 92 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7403 (ttp80) REVERT: s 9 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7266 (mptt) REVERT: 3 24 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7298 (ptp-170) outliers start: 193 outliers final: 127 residues processed: 985 average time/residue: 2.4223 time to fit residues: 3315.1734 Evaluate side-chains 1008 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 855 time to evaluate : 6.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 189 VAL Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 167 VAL Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 9 GLU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 VAL Chi-restraints excluded: chain i residue 85 LYS Chi-restraints excluded: chain i residue 96 ARG Chi-restraints excluded: chain i residue 128 ASN Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 53 LYS Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 9 LYS Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 70 ILE Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 866 optimal weight: 6.9990 chunk 912 optimal weight: 20.0000 chunk 832 optimal weight: 10.0000 chunk 887 optimal weight: 1.9990 chunk 534 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 696 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 801 optimal weight: 3.9990 chunk 839 optimal weight: 4.9990 chunk 884 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN D 40 GLN F 17 GLN F 46 GLN F 55 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 40 GLN ** Q 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 ASN c 115 GLN j 3 GLN l 60 GLN m 18 GLN o 10 GLN o 41 GLN t 27 ASN t 40 ASN w 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 153921 Z= 0.190 Angle : 0.669 14.176 230344 Z= 0.364 Chirality : 0.037 0.365 29320 Planarity : 0.007 0.134 12255 Dihedral : 23.008 178.224 77173 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 3.00 % Allowed : 18.22 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5474 helix: 0.98 (0.12), residues: 1902 sheet: -0.36 (0.15), residues: 1117 loop : -0.67 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP w 39 HIS 0.007 0.001 HIS M 14 PHE 0.029 0.002 PHE F 78 TYR 0.017 0.002 TYR r 38 ARG 0.008 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 859 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.4703 (tp30) REVERT: D 104 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5505 (mtt90) REVERT: D 128 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.3907 (ttt90) REVERT: D 178 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.4809 (mtm) REVERT: E 16 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.6260 (pp) REVERT: F 14 GLN cc_start: 0.5487 (OUTLIER) cc_final: 0.4020 (mp-120) REVERT: G 79 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5301 (ttt90) REVERT: G 116 MET cc_start: 0.7730 (tpt) cc_final: 0.7395 (tpt) REVERT: H 96 MET cc_start: 0.6846 (ptp) cc_final: 0.6388 (ttp) REVERT: I 88 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5147 (mpp) REVERT: L 9 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6874 (ttm110) REVERT: N 53 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6493 (ptp-170) REVERT: Q 33 ILE cc_start: 0.7591 (pt) cc_final: 0.7383 (pt) REVERT: Q 40 ARG cc_start: 0.7351 (mmm160) cc_final: 0.7078 (mmm160) REVERT: S 48 THR cc_start: 0.6409 (OUTLIER) cc_final: 0.6086 (m) REVERT: T 24 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5781 (mtt-85) REVERT: c 23 GLU cc_start: 0.6014 (pt0) cc_final: 0.5767 (pt0) REVERT: c 251 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7269 (tp40) REVERT: j 4 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: j 19 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8098 (m) REVERT: l 55 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6787 (ttm-80) REVERT: l 75 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6420 (mm-30) REVERT: n 20 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6600 (pt0) REVERT: p 110 VAL cc_start: 0.8277 (p) cc_final: 0.8046 (t) REVERT: p 111 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: r 92 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: v 83 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6538 (pt0) REVERT: 3 24 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6480 (ptp-170) outliers start: 137 outliers final: 90 residues processed: 947 average time/residue: 2.3584 time to fit residues: 3092.9120 Evaluate side-chains 946 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 836 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain j residue 4 GLU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 20 ASP Chi-restraints excluded: chain 3 residue 24 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 582 optimal weight: 9.9990 chunk 938 optimal weight: 0.0370 chunk 572 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 984 optimal weight: 20.0000 chunk 905 optimal weight: 10.0000 chunk 783 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 overall best weight: 7.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN F 46 GLN F 55 HIS G 148 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 35 GLN O 40 GLN Q 51 ASN c 70 ASN c 115 GLN e 115 GLN e 136 GLN j 3 GLN l 60 GLN m 18 GLN o 10 GLN ** o 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN w 6 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 153921 Z= 0.355 Angle : 0.846 18.978 230344 Z= 0.438 Chirality : 0.044 0.330 29320 Planarity : 0.008 0.149 12255 Dihedral : 23.141 179.420 77173 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.02 % Allowed : 18.57 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 5474 helix: 0.64 (0.12), residues: 1901 sheet: -0.38 (0.15), residues: 1102 loop : -0.78 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP w 39 HIS 0.011 0.002 HIS M 14 PHE 0.038 0.003 PHE F 78 TYR 0.023 0.003 TYR p 32 ARG 0.011 0.001 ARG p 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10948 Ramachandran restraints generated. 5474 Oldfield, 0 Emsley, 5474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 852 time to evaluate : 6.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.4814 (tp30) REVERT: C 93 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5265 (m-30) REVERT: D 104 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5515 (mtt90) REVERT: D 113 GLU cc_start: 0.5805 (mm-30) cc_final: 0.5572 (mm-30) REVERT: D 128 ARG cc_start: 0.5069 (OUTLIER) cc_final: 0.3973 (ttt90) REVERT: D 178 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.4750 (mtm) REVERT: E 16 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.6444 (pp) REVERT: F 14 GLN cc_start: 0.5568 (OUTLIER) cc_final: 0.3508 (mp-120) REVERT: F 102 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.4197 (mpt) REVERT: G 79 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5206 (ttt90) REVERT: G 116 MET cc_start: 0.7763 (tpt) cc_final: 0.7374 (tpt) REVERT: H 31 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6215 (mmpt) REVERT: H 96 MET cc_start: 0.7000 (ptp) cc_final: 0.6511 (ttp) REVERT: I 88 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5143 (mpp) REVERT: L 9 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6847 (ttm110) REVERT: N 53 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6349 (ptp-170) REVERT: O 84 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6248 (ttp80) REVERT: c 23 GLU cc_start: 0.6180 (pt0) cc_final: 0.5942 (pt0) REVERT: c 251 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7446 (tp40) REVERT: d 28 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: l 55 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6805 (ttm-80) REVERT: l 75 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: n 20 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: p 111 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: r 92 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7387 (ttp80) REVERT: 3 24 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6811 (ptp-170) outliers start: 138 outliers final: 104 residues processed: 935 average time/residue: 2.3957 time to fit residues: 3097.0690 Evaluate side-chains 972 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 847 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 197 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 145 LYS Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain o residue 80 VAL Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 108 SER Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain v residue 81 SER Chi-restraints excluded: chain v residue 83 GLU Chi-restraints excluded: chain w residue 62 LYS Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 20 ASN Chi-restraints excluded: chain x residue 40 SER Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 56 LYS Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 47 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 24 ARG Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 622 optimal weight: 10.0000 chunk 834 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 722 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 785 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 806 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS D 36 GLN F 11 HIS F 17 GLN F 46 GLN F 55 HIS G 148 ASN K 81 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN O 40 GLN Q 51 ASN c 70 ASN c 115 GLN e 115 GLN e 136 GLN j 3 GLN l 60 GLN m 18 GLN o 10 GLN t 40 ASN w 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140641 restraints weight = 127038.235| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 0.63 r_work: 0.3205 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 153921 Z= 0.319 Angle : 0.810 18.505 230344 Z= 0.424 Chirality : 0.043 0.339 29320 Planarity : 0.008 0.148 12255 Dihedral : 23.138 179.146 77173 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 3.11 % Allowed : 18.72 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5474 helix: 0.62 (0.12), residues: 1901 sheet: -0.40 (0.15), residues: 1105 loop : -0.79 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP w 39 HIS 0.012 0.002 HIS o 77 PHE 0.049 0.003 PHE F 78 TYR 0.022 0.002 TYR p 32 ARG 0.012 0.001 ARG 4 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44018.05 seconds wall clock time: 763 minutes 12.75 seconds (45792.75 seconds total)